Download OpenAPI specification:Download
Provides programmatic access to information and annotations stored in the Protein Data Bank.
Models are generated from JSON schema version: 1.48.1.
API services deployed on: Mon, 27 Jan 2025 11:33:45 -0800
entry_id required | string Example: 1RH7 ENTRY ID of the entry. |
assembly_id required | string Example: 1 ASSEMBLY ID of the biological assembly candidate. |
{- "pdbx_struct_assembly": {
- "details": "The icosahedral virus particle.\n",
- "id": "string",
- "method_details": "string",
- "oligomeric_count": 0,
- "oligomeric_details": "monomer, octameric, tetradecameric, eicosameric, 21-meric, 60-meric, 180-meric, helical\n",
- "rcsb_candidate_assembly": "Y\n",
- "rcsb_details": "author_and_software_defined_assembly\n"
}, - "pdbx_struct_assembly_auth_evidence": [
- {
- "assembly_id": "string",
- "details": "Homology to bacteriorhodopsin, Helical filament was observed by negative staining and Cryo-EM\n",
- "experimental_support": "NMR Distance Restraints",
- "id": "string"
}
], - "pdbx_struct_assembly_gen": [
- {
- "assembly_id": "string",
- "asym_id_list": [
- "string"
], - "oper_expression": "(1), (1,2,5), (1-60), (1-60)(61)\n",
- "ordinal": 0
}
], - "pdbx_struct_assembly_prop": [
- {
- "assembly_id": "string",
- "biol_id": "string",
- "type": "ABSA (A^2)",
- "value": "string"
}
], - "pdbx_struct_oper_list": [
- {
- "id": "string",
- "matrix_1_1": 0.1,
- "matrix_1_2": 0.1,
- "matrix_1_3": 0.1,
- "matrix_2_1": 0.1,
- "matrix_2_2": 0.1,
- "matrix_2_3": 0.1,
- "matrix_3_1": 0.1,
- "matrix_3_2": 0.1,
- "matrix_3_3": 0.1,
- "name": "1_555, two-fold rotation\n",
- "symmetry_operation": "x,y,z, x+1/2,y,-z\n",
- "type": "2D crystal symmetry operation",
- "vector_1": 0.1,
- "vector_2": 0.1,
- "vector_3": 0.1
}
], - "rcsb_assembly_container_identifiers": {
- "assembly_id": "1, 5\n",
- "entry_id": "string",
- "rcsb_id": "1KIP-1\n",
- "interface_ids": [
- "string"
]
}, - "rcsb_assembly_info": {
- "assembly_id": "string",
- "atom_count": 0,
- "branched_atom_count": 0,
- "branched_entity_count": 0,
- "branched_entity_instance_count": 0,
- "deuterated_water_count": 0,
- "entry_id": "1KIP\n",
- "hydrogen_atom_count": 0,
- "modeled_polymer_monomer_count": 0,
- "na_polymer_entity_types": "DNA (only)\n",
- "nonpolymer_atom_count": 0,
- "nonpolymer_entity_count": 0,
- "nonpolymer_entity_instance_count": 0,
- "polymer_atom_count": 0,
- "polymer_composition": "homomeric protein\n",
- "polymer_entity_count": 0,
- "polymer_entity_count_DNA": 0,
- "polymer_entity_count_RNA": 0,
- "polymer_entity_count_nucleic_acid": 0,
- "polymer_entity_count_nucleic_acid_hybrid": 0,
- "polymer_entity_count_protein": 0,
- "polymer_entity_instance_count": 0,
- "polymer_entity_instance_count_DNA": 0,
- "polymer_entity_instance_count_RNA": 0,
- "polymer_entity_instance_count_nucleic_acid": 0,
- "polymer_entity_instance_count_nucleic_acid_hybrid": 0,
- "polymer_entity_instance_count_protein": 0,
- "polymer_monomer_count": 0,
- "selected_polymer_entity_types": "Protein (only)\n",
- "solvent_atom_count": 0,
- "solvent_entity_count": 0,
- "solvent_entity_instance_count": 0,
- "unmodeled_polymer_monomer_count": 0,
- "num_interfaces": 0,
- "num_interface_entities": 0,
- "num_homomeric_interface_entities": 0,
- "num_heteromeric_interface_entities": 0,
- "num_isologous_interface_entities": 0,
- "num_heterologous_interface_entities": 0,
- "num_protein_interface_entities": 0,
- "num_na_interface_entities": 0,
- "num_prot-na_interface_entities": 0,
- "total_assembly_buried_surface_area": 0.1,
- "total_number_interface_residues": 0
}, - "rcsb_id": "1KIP-1\n",
- "rcsb_struct_symmetry": [
- {
- "symbol": "C1, D3, H\n",
- "type": "Asymmetric",
- "stoichiometry": [
- "string"
], - "oligomeric_state": "Monomer, Homo 2-mer, Hetero 3-mer\n",
- "clusters": [
- {
- "members": [
- {
- "asym_id": "string",
- "pdbx_struct_oper_list_ids": [
- "string"
]
}
], - "avg_rmsd": 0.1
}
], - "rotation_axes": [
- {
- "start": [
- 0.1,
- 0.1,
- 0.1
], - "end": [
- 0.1,
- 0.1,
- 0.1
], - "order": 0
}
], - "kind": "Global Symmetry"
}
], - "rcsb_struct_symmetry_provenance_code": "string",
- "rcsb_struct_symmetry_lineage": [
- {
- "id": "Global Symmetry.Cyclic.C2.Homo 2-mer\n",
- "name": "Asymmetric, Global Symmetry, C1, Hetero 3-mer\n",
- "depth": 0
}
], - "rcsb_assembly_feature": [
- {
- "assignment_version": "string",
- "description": "string",
- "feature_id": "string",
- "name": "string",
- "provenance_source": "MCSA\n",
- "type": "MCSA",
- "feature_positions": [
- {
- "beg_seq_id": 0,
- "end_seq_id": 0,
- "values": [
- 0.1
], - "asym_id": "A, B\n",
- "struct_oper_list": [
- "string"
]
}
], - "additional_properties": [
- {
- "name": "MCSA_MOTIF_COMPATIBILITY",
- "values": [
- { }
]
}
]
}
], - "rcsb_assembly_annotation": [
- {
- "annotation_id": "string",
- "assignment_version": "string",
- "description": "string",
- "name": "string",
- "provenance_source": "MCSA\n",
- "type": "MCSA",
- "additional_properties": [
- {
- "name": "MCSA_MOTIF_COMPATIBILITY",
- "values": [
- { }
]
}
]
}
], - "rcsb_latest_revision": {
- "major_revision": 0,
- "minor_revision": 0,
- "revision_date": "2019-08-24T14:15:22Z"
}
}
provides access to information about structures at the level of unique molecular entities
entry_id required | string Example: 4CYG ID of the entry that needs to be fetched. |
entity_id required | string Example: 2 ID of the entity that needs to be fetched. |
{- "rcsb_cluster_membership": [
- {
- "cluster_id": 0,
- "identity": 0
}
], - "entity_poly": {
- "nstd_linkage": "n",
- "nstd_monomer": "n",
- "pdbx_seq_one_letter_code": "HHHH(MSE)AKQRSG or AUCGGAAU, (MSE)SHHWGYGKHNGPEHWHKDFPIAKGERQSPVDIDTHTAKYDPSLKPLSVSYDQATSLRILNNGAAFNVEFD\n",
- "pdbx_seq_one_letter_code_can": "MSHHWGYGKHNGPEHWHKDFPIAKGERQSPVDIDTHTAKYDPSLKPLSVSYDQATSLRILNNGAAFNVEFD\n",
- "pdbx_sequence_evidence_code": "depositor provided",
- "pdbx_strand_id": "A,B, A, B, A,B,C\n",
- "pdbx_target_identifier": "JCSG-11211, 356560\n",
- "rcsb_artifact_monomer_count": 0,
- "rcsb_conflict_count": 0,
- "rcsb_deletion_count": 0,
- "rcsb_entity_polymer_type": "DNA",
- "rcsb_insertion_count": 0,
- "rcsb_mutation_count": 0,
- "rcsb_non_std_monomer_count": 0,
- "rcsb_non_std_monomers": [
- "string"
], - "rcsb_prd_id": "string",
- "rcsb_sample_sequence_length": 0,
- "type": "cyclic-pseudo-peptide"
}, - "entity_src_gen": [
- {
- "expression_system_id": "string",
- "gene_src_common_name": "man, yeast, bacteria\n",
- "gene_src_details": "string",
- "gene_src_genus": "Homo, Saccharomyces, Escherichia\n",
- "gene_src_species": "sapiens, cerevisiae, coli\n",
- "gene_src_strain": "DH5a, BMH 71-18\n",
- "gene_src_tissue": "heart, liver, eye lens\n",
- "gene_src_tissue_fraction": "mitochondria, nucleus, membrane\n",
- "host_org_common_name": "yeast, bacteria\n",
- "host_org_details": "string",
- "host_org_genus": "Saccharomyces, Escherichia\n",
- "host_org_species": "cerevisiae, coli\n",
- "pdbx_alt_source_flag": "model",
- "pdbx_beg_seq_num": 0,
- "pdbx_description": "string",
- "pdbx_end_seq_num": 0,
- "pdbx_gene_src_atcc": "6051",
- "pdbx_gene_src_cell": "ENDOTHELIAL\n",
- "pdbx_gene_src_cell_line": "HELA CELLS\n",
- "pdbx_gene_src_cellular_location": "CYTOPLASM, NUCLEUS\n",
- "pdbx_gene_src_fragment": "CYTOPLASM, NUCLEUS\n",
- "pdbx_gene_src_gene": "string",
- "pdbx_gene_src_ncbi_taxonomy_id": "string",
- "pdbx_gene_src_organ": "KIDNEY, LIVER, PANCREAS\n",
- "pdbx_gene_src_organelle": "MITOCHONDRIA\n",
- "pdbx_gene_src_scientific_name": "Homo sapiens, Saccharomyces Cerevisiae\n",
- "pdbx_gene_src_variant": "DELTAH1DELTATRP\n",
- "pdbx_host_org_atcc": "string",
- "pdbx_host_org_cell": "ENDOTHELIAL\n",
- "pdbx_host_org_cell_line": "HELA\n",
- "pdbx_host_org_cellular_location": "CYTOPLASM, NUCLEUS\n",
- "pdbx_host_org_culture_collection": "string",
- "pdbx_host_org_gene": "HIV-1 POL, GLNS7, U1A (2-98, Y31H, Q36R)\n",
- "pdbx_host_org_ncbi_taxonomy_id": "string",
- "pdbx_host_org_organ": "KIDNEY\n",
- "pdbx_host_org_organelle": "MITOCHONDRIA\n",
- "pdbx_host_org_scientific_name": "ESCHERICHIA COLI, SACCHAROMYCES CEREVISIAE\n",
- "pdbx_host_org_strain": "AR120\n",
- "pdbx_host_org_tissue": "heart, liver, eye lens\n",
- "pdbx_host_org_tissue_fraction": "mitochondria, nucleus, membrane\n",
- "pdbx_host_org_variant": "TRP-LAC, LAMBDA DE3\n",
- "pdbx_host_org_vector": "PBIT36, PET15B, PUC18\n",
- "pdbx_host_org_vector_type": "COSMID, PLASMID\n",
- "pdbx_seq_type": "Biological sequence",
- "pdbx_src_id": 0,
- "plasmid_details": "string",
- "plasmid_name": "pET3C, pT123sab\n"
}
], - "entity_src_nat": [
- {
- "common_name": "man, yeast, bacteria\n",
- "details": "string",
- "genus": "Homo, Saccharomyces, Escherichia\n",
- "pdbx_alt_source_flag": "model",
- "pdbx_atcc": "6051",
- "pdbx_beg_seq_num": 0,
- "pdbx_cell": "BHK-21\n",
- "pdbx_cell_line": "HELA\n",
- "pdbx_cellular_location": "string",
- "pdbx_end_seq_num": 0,
- "pdbx_fragment": "string",
- "pdbx_ncbi_taxonomy_id": "string",
- "pdbx_organ": "KIDNEY\n",
- "pdbx_organelle": "MITOCHONDRIA\n",
- "pdbx_organism_scientific": "Bos taurus, BOS TAURUS, SUS SCROFA, ASPERGILLUS ORYZAE\n",
- "pdbx_plasmid_details": "PLC28 DERIVATIVE\n",
- "pdbx_plasmid_name": "pB322\n",
- "pdbx_secretion": "saliva, urine, venom\n",
- "pdbx_src_id": 0,
- "pdbx_variant": "string",
- "species": "sapiens, cerevisiae, coli\n",
- "strain": "DH5a, BMH 71-18\n",
- "tissue": "heart, liver, eye lens\n",
- "tissue_fraction": "mitochondria, nucleus, membrane\n"
}
], - "pdbx_entity_src_syn": [
- {
- "details": "This sequence occurs naturally in humans.\n",
- "ncbi_taxonomy_id": "string",
- "organism_common_name": "house mouse\n",
- "organism_scientific": "synthetic construct, Mus musculus\n",
- "pdbx_alt_source_flag": "model",
- "pdbx_beg_seq_num": 0,
- "pdbx_end_seq_num": 0,
- "pdbx_src_id": 0
}
], - "rcsb_entity_host_organism": [
- {
- "beg_seq_num": 0,
- "common_name": "string",
- "end_seq_num": 0,
- "ncbi_common_names": [
- "string"
], - "ncbi_parent_scientific_name": "string",
- "ncbi_scientific_name": "string",
- "ncbi_taxonomy_id": 0,
- "pdbx_src_id": 0,
- "provenance_source": "PDB Primary Data",
- "scientific_name": "string",
- "taxonomy_lineage": [
- {
- "depth": 0,
- "id": "469008, 10469\n",
- "name": "Escherichia coli BL21(DE3), Baculovirus\n"
}
]
}
], - "rcsb_entity_source_organism": [
- {
- "beg_seq_num": 0,
- "common_name": "string",
- "end_seq_num": 0,
- "ncbi_common_names": [
- "string"
], - "ncbi_parent_scientific_name": "Archaea, Bacteria, Eukaryota, Adnaviria, Bicaudaviridae, Clavaviridae, Duplodnaviria\n",
- "ncbi_scientific_name": "string",
- "ncbi_taxonomy_id": 0,
- "pdbx_src_id": 0,
- "provenance_source": "NCBI",
- "scientific_name": "string",
- "source_type": "genetically engineered",
- "taxonomy_lineage": [
- {
- "depth": 0,
- "id": "9606, 10090\n",
- "name": "Homo sapiens, Mus musculus\n"
}
], - "rcsb_gene_name": [
- {
- "provenance_source": "NCBI",
- "value": "lacA, hemH\n"
}
]
}
], - "rcsb_polymer_entity": {
- "details": "string",
- "formula_weight": 0.1,
- "pdbx_description": "Green fluorescent protein, 23S ribosomal RNA, NAD-dependent protein deacylase sirtuin-5, mitochondrial\n",
- "pdbx_ec": "2.7.7.7\n",
- "pdbx_fragment": "KLENOW FRAGMENT, REPLICASE OPERATOR HAIRPIN, C-TERMINAL DOMAIN\n",
- "pdbx_mutation": "Y31H, DEL(298-323)\n",
- "pdbx_number_of_molecules": 0,
- "rcsb_multiple_source_flag": "N",
- "rcsb_source_part_count": 0,
- "rcsb_source_taxonomy_count": 0,
- "src_method": "man",
- "rcsb_ec_lineage": [
- {
- "depth": 0,
- "id": "2, 2.7.1.153\n",
- "name": "Transferases, phosphatidylinositol-4,5-bisphosphate 3-kinase\n"
}
], - "rcsb_macromolecular_names_combined": [
- {
- "name": "Lysozyme C, Plasmid recombination enzyme, Pyruvate carboxylase\n",
- "provenance_code": "string",
- "provenance_source": "PDB Preferred Name"
}
], - "rcsb_enzyme_class_combined": [
- {
- "depth": 0,
- "ec": "string",
- "provenance_source": "PDB Primary Data"
}
], - "rcsb_polymer_name_combined": {
- "names": [
- "string"
], - "provenance_source": "PDB Preferred Name"
}
}, - "rcsb_polymer_entity_align": [
- {
- "provenance_source": "PDB, SIFTS, RCSB\n",
- "reference_database_accession": "Q9HD40\n",
- "reference_database_isoform": "P01116-2\n",
- "reference_database_name": "UniProt, GenBank, PDB\n",
- "aligned_regions": [
- {
- "entity_beg_seq_id": 0,
- "length": 0,
- "ref_beg_seq_id": 0
}
]
}
], - "rcsb_polymer_entity_annotation": [
- {
- "annotation_id": "string",
- "assignment_version": "V4_0_2\n",
- "description": "string",
- "name": "string",
- "provenance_source": "PDB, UniProt\n",
- "type": "GO, Pfam\n",
- "annotation_lineage": [
- {
- "depth": 0,
- "id": "string",
- "name": "string"
}
], - "additional_properties": [
- {
- "name": "CARD_ARO_CATEGORY\n",
- "values": [
- { }
]
}
]
}
], - "rcsb_polymer_entity_container_identifiers": {
- "asym_ids": [
- "string"
], - "auth_asym_ids": [
- "string"
], - "chem_comp_monomers": [
- "string"
], - "chem_comp_nstd_monomers": [
- "string"
], - "chem_ref_def_id": "PRD_000010\n",
- "entity_id": "1, 2\n",
- "entry_id": "4HHB, 1KIP\n",
- "prd_id": "PRD_000010\n",
- "rcsb_id": "6EL3_1\n",
- "reference_sequence_identifiers": [
- {
- "database_accession": "P01116, 55771382\n",
- "database_isoform": "P01116-2\n",
- "database_name": "UniProt, GenBank\n",
- "entity_sequence_coverage": 0.1,
- "provenance_source": "PDB, SIFTS\n",
- "reference_sequence_coverage": 0.1
}
], - "uniprot_ids": [
- "string"
]
}, - "rcsb_polymer_entity_feature": [
- {
- "assignment_version": "V4_0_2\n",
- "description": "string",
- "feature_id": "string",
- "name": "string",
- "provenance_source": "PDB\n",
- "reference_scheme": "PDB entity, UniProt, NCBI\n",
- "type": "mutation, artifact\n",
- "feature_positions": [
- {
- "beg_comp_id": "TRP, VAL\n",
- "beg_seq_id": 0,
- "end_seq_id": 0,
- "value": 0.1,
- "values": [
- 0.1
]
}
], - "additional_properties": [
- {
- "name": "PARENT_COMP_ID\n",
- "values": [
- { }
]
}
]
}
], - "rcsb_polymer_entity_feature_summary": [
- {
- "count": 0,
- "coverage": 0.1,
- "maximum_length": 0,
- "maximum_value": 0.1,
- "minimum_length": 0,
- "minimum_value": 0.1,
- "type": "mutation, artifact\n"
}
], - "rcsb_polymer_entity_keywords": {
- "text": "string"
}, - "rcsb_polymer_entity_name_com": [
- {
- "name": "HIV protease monomer, hemoglobin alpha chain\n"
}
], - "rcsb_polymer_entity_name_sys": [
- {
- "name": "string",
- "system": "Chemical Abstracts conventions\n"
}
], - "rcsb_related_target_references": [
- {
- "related_resource_name": "DrugBank, ChEMBL, Pharos\n",
- "related_resource_version": "6.11.0\n",
- "related_target_id": "string",
- "target_taxonomy_id": 0,
- "aligned_target": [
- {
- "entity_beg_seq_id": 0,
- "length": 0,
- "target_beg_seq_id": 0
}
]
}
], - "rcsb_target_cofactors": [
- {
- "binding_assay_value": 0.1,
- "binding_assay_value_type": "pIC50, pEC50\n",
- "cofactor_InChIKey": "BNOCDEBUFVJMQI-REOHCLBHSA-N\n",
- "cofactor_SMILES": "OC(=O)[CH](CF)O[P](O)(O)=O\n",
- "cofactor_chem_comp_id": "0Z3, CD9\n",
- "cofactor_description": "A synthetic naphthoquinone without the isoprenoid side chain and biological activity,\n but can be converted to active vitamin K2, menaquinone, after alkylation in vivo.\n",
- "cofactor_name": "Menadione\n",
- "cofactor_prd_id": "PRD_000010\n",
- "cofactor_resource_id": "CHEMBL1987, DB00170\n",
- "mechanism_of_action": "Menadione (vitamin K3) is involved as a cofactor in the posttranslational gamma-carboxylation of glutamic acid residues of certain proteins i\nn the body. These proteins include the vitamin K-dependent coagulation factors II (prothrombin), VII (proconvertin), IX (Christmas factor), X (Stuart factor), protein\nC, protein S, protein Zv and a growth-arrest-specific factor (Gas6).\n",
- "neighbor_flag": "Y, N\n",
- "patent_nos": [
- "string"
], - "pubmed_ids": [
- 0
], - "resource_name": "DrugBank, ChEMBL, Pharos\n",
- "resource_version": "V4_0_2\n",
- "target_resource_id": "P00734, CHEMBL2242\n"
}
], - "rcsb_id": "6EL3_1\n",
- "rcsb_polymer_entity_group_membership": [
- {
- "group_id": "1_100, P00003\n",
- "aggregation_method": "sequence_identity",
- "similarity_cutoff": 0.1,
- "aligned_regions": [
- {
- "entity_beg_seq_id": 0,
- "length": 0,
- "ref_beg_seq_id": 0
}
]
}
], - "rcsb_genomic_lineage": [
- {
- "id": "9606, 568815441, 414325\n",
- "name": "Homo sapiens, 8, defensin beta 103A\n",
- "depth": 0
}
], - "rcsb_membrane_lineage": [
- {
- "id": "MONOTOPIC MEMBRANE PROTEINS.Oxidases.Monoamine Oxidase A\n",
- "name": "string",
- "depth": 0
}
], - "rcsb_membrane_lineage_provenance_code": "Mpstruc",
- "rcsb_cluster_flexibility": {
- "link": "string",
- "label": "string",
- "avg_rmsd": 0.1,
- "max_rmsd": 0.1,
- "provenance_code": "PDBFlex"
}, - "rcsb_latest_revision": {
- "major_revision": 0,
- "minor_revision": 0,
- "revision_date": "2019-08-24T14:15:22Z"
}
}
entry_id required | string Example: 4G22 ENTRY ID of the entry. |
entity_id required | string Example: 2 ENTITY ID of the non-polymer entity. |
{- "pdbx_entity_nonpoly": {
- "comp_id": "string",
- "entity_id": "string",
- "name": "string",
- "rcsb_prd_id": "string"
}, - "rcsb_nonpolymer_entity": {
- "details": "string",
- "formula_weight": 0.1,
- "pdbx_description": "string",
- "pdbx_number_of_molecules": 0
}, - "rcsb_nonpolymer_entity_annotation": [
- {
- "annotation_id": "string",
- "assignment_version": "V4_0_2\n",
- "comp_id": "GTP, STN\n",
- "description": "string",
- "name": "string",
- "provenance_source": "PDB\n",
- "type": "SUBJECT_OF_INVESTIGATION\n",
- "annotation_lineage": [
- {
- "depth": 0,
- "id": "string",
- "name": "string"
}
]
}
], - "rcsb_nonpolymer_entity_container_identifiers": {
- "asym_ids": [
- "string"
], - "auth_asym_ids": [
- "string"
], - "chem_ref_def_id": "PRD_000010\n",
- "entity_id": "1, 2\n",
- "entry_id": "4HHB, 1KIP\n",
- "nonpolymer_comp_id": "GTP, STN\n",
- "prd_id": "PRD_000010\n",
- "rcsb_id": "6EL3_1\n",
- "reference_chemical_identifiers_provenance_source": "PDB",
- "reference_chemical_identifiers_resource_accession": [
- "string"
], - "reference_chemical_identifiers_resource_name": "ChEBI"
}, - "rcsb_nonpolymer_entity_feature": [
- {
- "assignment_version": "V4_0_2\n",
- "comp_id": "GTP, STN\n",
- "description": "string",
- "feature_id": "string",
- "name": "string",
- "provenance_source": "PDB\n",
- "type": "SUBJECT_OF_INVESTIGATION\n",
- "value": 0.1,
- "additional_properties": [
- {
- "name": "string",
- "values": [
- { }
]
}
]
}
], - "rcsb_nonpolymer_entity_feature_summary": [
- {
- "comp_id": "GTP, STN\n",
- "count": 0,
- "maximum_length": 0,
- "maximum_value": 0.1,
- "minimum_length": 0,
- "minimum_value": 0.1,
- "type": "SUBJECT_OF_INVESTIGATION\n"
}
], - "rcsb_nonpolymer_entity_keywords": {
- "text": "string"
}, - "rcsb_nonpolymer_entity_name_com": [
- {
- "name": "string"
}
], - "rcsb_id": "6EL3_1\n",
- "rcsb_latest_revision": {
- "major_revision": 0,
- "minor_revision": 0,
- "revision_date": "2019-08-24T14:15:22Z"
}
}
entry_id required | string Example: 4G22 ENTRY ID of the entry. |
entity_id required | string Example: 1 ENTITY ID of the polymer entity. |
{- "rcsb_cluster_membership": [
- {
- "cluster_id": 0,
- "identity": 0
}
], - "entity_poly": {
- "nstd_linkage": "n",
- "nstd_monomer": "n",
- "pdbx_seq_one_letter_code": "HHHH(MSE)AKQRSG or AUCGGAAU, (MSE)SHHWGYGKHNGPEHWHKDFPIAKGERQSPVDIDTHTAKYDPSLKPLSVSYDQATSLRILNNGAAFNVEFD\n",
- "pdbx_seq_one_letter_code_can": "MSHHWGYGKHNGPEHWHKDFPIAKGERQSPVDIDTHTAKYDPSLKPLSVSYDQATSLRILNNGAAFNVEFD\n",
- "pdbx_sequence_evidence_code": "depositor provided",
- "pdbx_strand_id": "A,B, A, B, A,B,C\n",
- "pdbx_target_identifier": "JCSG-11211, 356560\n",
- "rcsb_artifact_monomer_count": 0,
- "rcsb_conflict_count": 0,
- "rcsb_deletion_count": 0,
- "rcsb_entity_polymer_type": "DNA",
- "rcsb_insertion_count": 0,
- "rcsb_mutation_count": 0,
- "rcsb_non_std_monomer_count": 0,
- "rcsb_non_std_monomers": [
- "string"
], - "rcsb_prd_id": "string",
- "rcsb_sample_sequence_length": 0,
- "type": "cyclic-pseudo-peptide"
}, - "entity_src_gen": [
- {
- "expression_system_id": "string",
- "gene_src_common_name": "man, yeast, bacteria\n",
- "gene_src_details": "string",
- "gene_src_genus": "Homo, Saccharomyces, Escherichia\n",
- "gene_src_species": "sapiens, cerevisiae, coli\n",
- "gene_src_strain": "DH5a, BMH 71-18\n",
- "gene_src_tissue": "heart, liver, eye lens\n",
- "gene_src_tissue_fraction": "mitochondria, nucleus, membrane\n",
- "host_org_common_name": "yeast, bacteria\n",
- "host_org_details": "string",
- "host_org_genus": "Saccharomyces, Escherichia\n",
- "host_org_species": "cerevisiae, coli\n",
- "pdbx_alt_source_flag": "model",
- "pdbx_beg_seq_num": 0,
- "pdbx_description": "string",
- "pdbx_end_seq_num": 0,
- "pdbx_gene_src_atcc": "6051",
- "pdbx_gene_src_cell": "ENDOTHELIAL\n",
- "pdbx_gene_src_cell_line": "HELA CELLS\n",
- "pdbx_gene_src_cellular_location": "CYTOPLASM, NUCLEUS\n",
- "pdbx_gene_src_fragment": "CYTOPLASM, NUCLEUS\n",
- "pdbx_gene_src_gene": "string",
- "pdbx_gene_src_ncbi_taxonomy_id": "string",
- "pdbx_gene_src_organ": "KIDNEY, LIVER, PANCREAS\n",
- "pdbx_gene_src_organelle": "MITOCHONDRIA\n",
- "pdbx_gene_src_scientific_name": "Homo sapiens, Saccharomyces Cerevisiae\n",
- "pdbx_gene_src_variant": "DELTAH1DELTATRP\n",
- "pdbx_host_org_atcc": "string",
- "pdbx_host_org_cell": "ENDOTHELIAL\n",
- "pdbx_host_org_cell_line": "HELA\n",
- "pdbx_host_org_cellular_location": "CYTOPLASM, NUCLEUS\n",
- "pdbx_host_org_culture_collection": "string",
- "pdbx_host_org_gene": "HIV-1 POL, GLNS7, U1A (2-98, Y31H, Q36R)\n",
- "pdbx_host_org_ncbi_taxonomy_id": "string",
- "pdbx_host_org_organ": "KIDNEY\n",
- "pdbx_host_org_organelle": "MITOCHONDRIA\n",
- "pdbx_host_org_scientific_name": "ESCHERICHIA COLI, SACCHAROMYCES CEREVISIAE\n",
- "pdbx_host_org_strain": "AR120\n",
- "pdbx_host_org_tissue": "heart, liver, eye lens\n",
- "pdbx_host_org_tissue_fraction": "mitochondria, nucleus, membrane\n",
- "pdbx_host_org_variant": "TRP-LAC, LAMBDA DE3\n",
- "pdbx_host_org_vector": "PBIT36, PET15B, PUC18\n",
- "pdbx_host_org_vector_type": "COSMID, PLASMID\n",
- "pdbx_seq_type": "Biological sequence",
- "pdbx_src_id": 0,
- "plasmid_details": "string",
- "plasmid_name": "pET3C, pT123sab\n"
}
], - "entity_src_nat": [
- {
- "common_name": "man, yeast, bacteria\n",
- "details": "string",
- "genus": "Homo, Saccharomyces, Escherichia\n",
- "pdbx_alt_source_flag": "model",
- "pdbx_atcc": "6051",
- "pdbx_beg_seq_num": 0,
- "pdbx_cell": "BHK-21\n",
- "pdbx_cell_line": "HELA\n",
- "pdbx_cellular_location": "string",
- "pdbx_end_seq_num": 0,
- "pdbx_fragment": "string",
- "pdbx_ncbi_taxonomy_id": "string",
- "pdbx_organ": "KIDNEY\n",
- "pdbx_organelle": "MITOCHONDRIA\n",
- "pdbx_organism_scientific": "Bos taurus, BOS TAURUS, SUS SCROFA, ASPERGILLUS ORYZAE\n",
- "pdbx_plasmid_details": "PLC28 DERIVATIVE\n",
- "pdbx_plasmid_name": "pB322\n",
- "pdbx_secretion": "saliva, urine, venom\n",
- "pdbx_src_id": 0,
- "pdbx_variant": "string",
- "species": "sapiens, cerevisiae, coli\n",
- "strain": "DH5a, BMH 71-18\n",
- "tissue": "heart, liver, eye lens\n",
- "tissue_fraction": "mitochondria, nucleus, membrane\n"
}
], - "pdbx_entity_src_syn": [
- {
- "details": "This sequence occurs naturally in humans.\n",
- "ncbi_taxonomy_id": "string",
- "organism_common_name": "house mouse\n",
- "organism_scientific": "synthetic construct, Mus musculus\n",
- "pdbx_alt_source_flag": "model",
- "pdbx_beg_seq_num": 0,
- "pdbx_end_seq_num": 0,
- "pdbx_src_id": 0
}
], - "rcsb_entity_host_organism": [
- {
- "beg_seq_num": 0,
- "common_name": "string",
- "end_seq_num": 0,
- "ncbi_common_names": [
- "string"
], - "ncbi_parent_scientific_name": "string",
- "ncbi_scientific_name": "string",
- "ncbi_taxonomy_id": 0,
- "pdbx_src_id": 0,
- "provenance_source": "PDB Primary Data",
- "scientific_name": "string",
- "taxonomy_lineage": [
- {
- "depth": 0,
- "id": "469008, 10469\n",
- "name": "Escherichia coli BL21(DE3), Baculovirus\n"
}
]
}
], - "rcsb_entity_source_organism": [
- {
- "beg_seq_num": 0,
- "common_name": "string",
- "end_seq_num": 0,
- "ncbi_common_names": [
- "string"
], - "ncbi_parent_scientific_name": "Archaea, Bacteria, Eukaryota, Adnaviria, Bicaudaviridae, Clavaviridae, Duplodnaviria\n",
- "ncbi_scientific_name": "string",
- "ncbi_taxonomy_id": 0,
- "pdbx_src_id": 0,
- "provenance_source": "NCBI",
- "scientific_name": "string",
- "source_type": "genetically engineered",
- "taxonomy_lineage": [
- {
- "depth": 0,
- "id": "9606, 10090\n",
- "name": "Homo sapiens, Mus musculus\n"
}
], - "rcsb_gene_name": [
- {
- "provenance_source": "NCBI",
- "value": "lacA, hemH\n"
}
]
}
], - "rcsb_polymer_entity": {
- "details": "string",
- "formula_weight": 0.1,
- "pdbx_description": "Green fluorescent protein, 23S ribosomal RNA, NAD-dependent protein deacylase sirtuin-5, mitochondrial\n",
- "pdbx_ec": "2.7.7.7\n",
- "pdbx_fragment": "KLENOW FRAGMENT, REPLICASE OPERATOR HAIRPIN, C-TERMINAL DOMAIN\n",
- "pdbx_mutation": "Y31H, DEL(298-323)\n",
- "pdbx_number_of_molecules": 0,
- "rcsb_multiple_source_flag": "N",
- "rcsb_source_part_count": 0,
- "rcsb_source_taxonomy_count": 0,
- "src_method": "man",
- "rcsb_ec_lineage": [
- {
- "depth": 0,
- "id": "2, 2.7.1.153\n",
- "name": "Transferases, phosphatidylinositol-4,5-bisphosphate 3-kinase\n"
}
], - "rcsb_macromolecular_names_combined": [
- {
- "name": "Lysozyme C, Plasmid recombination enzyme, Pyruvate carboxylase\n",
- "provenance_code": "string",
- "provenance_source": "PDB Preferred Name"
}
], - "rcsb_enzyme_class_combined": [
- {
- "depth": 0,
- "ec": "string",
- "provenance_source": "PDB Primary Data"
}
], - "rcsb_polymer_name_combined": {
- "names": [
- "string"
], - "provenance_source": "PDB Preferred Name"
}
}, - "rcsb_polymer_entity_align": [
- {
- "provenance_source": "PDB, SIFTS, RCSB\n",
- "reference_database_accession": "Q9HD40\n",
- "reference_database_isoform": "P01116-2\n",
- "reference_database_name": "UniProt, GenBank, PDB\n",
- "aligned_regions": [
- {
- "entity_beg_seq_id": 0,
- "length": 0,
- "ref_beg_seq_id": 0
}
]
}
], - "rcsb_polymer_entity_annotation": [
- {
- "annotation_id": "string",
- "assignment_version": "V4_0_2\n",
- "description": "string",
- "name": "string",
- "provenance_source": "PDB, UniProt\n",
- "type": "GO, Pfam\n",
- "annotation_lineage": [
- {
- "depth": 0,
- "id": "string",
- "name": "string"
}
], - "additional_properties": [
- {
- "name": "CARD_ARO_CATEGORY\n",
- "values": [
- { }
]
}
]
}
], - "rcsb_polymer_entity_container_identifiers": {
- "asym_ids": [
- "string"
], - "auth_asym_ids": [
- "string"
], - "chem_comp_monomers": [
- "string"
], - "chem_comp_nstd_monomers": [
- "string"
], - "chem_ref_def_id": "PRD_000010\n",
- "entity_id": "1, 2\n",
- "entry_id": "4HHB, 1KIP\n",
- "prd_id": "PRD_000010\n",
- "rcsb_id": "6EL3_1\n",
- "reference_sequence_identifiers": [
- {
- "database_accession": "P01116, 55771382\n",
- "database_isoform": "P01116-2\n",
- "database_name": "UniProt, GenBank\n",
- "entity_sequence_coverage": 0.1,
- "provenance_source": "PDB, SIFTS\n",
- "reference_sequence_coverage": 0.1
}
], - "uniprot_ids": [
- "string"
]
}, - "rcsb_polymer_entity_feature": [
- {
- "assignment_version": "V4_0_2\n",
- "description": "string",
- "feature_id": "string",
- "name": "string",
- "provenance_source": "PDB\n",
- "reference_scheme": "PDB entity, UniProt, NCBI\n",
- "type": "mutation, artifact\n",
- "feature_positions": [
- {
- "beg_comp_id": "TRP, VAL\n",
- "beg_seq_id": 0,
- "end_seq_id": 0,
- "value": 0.1,
- "values": [
- 0.1
]
}
], - "additional_properties": [
- {
- "name": "PARENT_COMP_ID\n",
- "values": [
- { }
]
}
]
}
], - "rcsb_polymer_entity_feature_summary": [
- {
- "count": 0,
- "coverage": 0.1,
- "maximum_length": 0,
- "maximum_value": 0.1,
- "minimum_length": 0,
- "minimum_value": 0.1,
- "type": "mutation, artifact\n"
}
], - "rcsb_polymer_entity_keywords": {
- "text": "string"
}, - "rcsb_polymer_entity_name_com": [
- {
- "name": "HIV protease monomer, hemoglobin alpha chain\n"
}
], - "rcsb_polymer_entity_name_sys": [
- {
- "name": "string",
- "system": "Chemical Abstracts conventions\n"
}
], - "rcsb_related_target_references": [
- {
- "related_resource_name": "DrugBank, ChEMBL, Pharos\n",
- "related_resource_version": "6.11.0\n",
- "related_target_id": "string",
- "target_taxonomy_id": 0,
- "aligned_target": [
- {
- "entity_beg_seq_id": 0,
- "length": 0,
- "target_beg_seq_id": 0
}
]
}
], - "rcsb_target_cofactors": [
- {
- "binding_assay_value": 0.1,
- "binding_assay_value_type": "pIC50, pEC50\n",
- "cofactor_InChIKey": "BNOCDEBUFVJMQI-REOHCLBHSA-N\n",
- "cofactor_SMILES": "OC(=O)[CH](CF)O[P](O)(O)=O\n",
- "cofactor_chem_comp_id": "0Z3, CD9\n",
- "cofactor_description": "A synthetic naphthoquinone without the isoprenoid side chain and biological activity,\n but can be converted to active vitamin K2, menaquinone, after alkylation in vivo.\n",
- "cofactor_name": "Menadione\n",
- "cofactor_prd_id": "PRD_000010\n",
- "cofactor_resource_id": "CHEMBL1987, DB00170\n",
- "mechanism_of_action": "Menadione (vitamin K3) is involved as a cofactor in the posttranslational gamma-carboxylation of glutamic acid residues of certain proteins i\nn the body. These proteins include the vitamin K-dependent coagulation factors II (prothrombin), VII (proconvertin), IX (Christmas factor), X (Stuart factor), protein\nC, protein S, protein Zv and a growth-arrest-specific factor (Gas6).\n",
- "neighbor_flag": "Y, N\n",
- "patent_nos": [
- "string"
], - "pubmed_ids": [
- 0
], - "resource_name": "DrugBank, ChEMBL, Pharos\n",
- "resource_version": "V4_0_2\n",
- "target_resource_id": "P00734, CHEMBL2242\n"
}
], - "rcsb_id": "6EL3_1\n",
- "rcsb_polymer_entity_group_membership": [
- {
- "group_id": "1_100, P00003\n",
- "aggregation_method": "sequence_identity",
- "similarity_cutoff": 0.1,
- "aligned_regions": [
- {
- "entity_beg_seq_id": 0,
- "length": 0,
- "ref_beg_seq_id": 0
}
]
}
], - "rcsb_genomic_lineage": [
- {
- "id": "9606, 568815441, 414325\n",
- "name": "Homo sapiens, 8, defensin beta 103A\n",
- "depth": 0
}
], - "rcsb_membrane_lineage": [
- {
- "id": "MONOTOPIC MEMBRANE PROTEINS.Oxidases.Monoamine Oxidase A\n",
- "name": "string",
- "depth": 0
}
], - "rcsb_membrane_lineage_provenance_code": "Mpstruc",
- "rcsb_cluster_flexibility": {
- "link": "string",
- "label": "string",
- "avg_rmsd": 0.1,
- "max_rmsd": 0.1,
- "provenance_code": "PDBFlex"
}, - "rcsb_latest_revision": {
- "major_revision": 0,
- "minor_revision": 0,
- "revision_date": "2019-08-24T14:15:22Z"
}
}
entry_id required | string Example: 4G22 ENTRY ID of the entry. |
entity_id required | string Example: 1 ENTITY ID of the polymer entity. |
[- {
- "rcsb_id": "string",
- "rcsb_uniprot_container_identifiers": {
- "uniprot_id": "string",
- "reference_sequence_identifiers": [
- {
- "database_accession": "string",
- "database_isoform": "string",
- "database_name": "string",
- "provenance_source": "string"
}
]
}, - "rcsb_uniprot_accession": [
- "string"
], - "rcsb_uniprot_entry_name": [
- "string"
], - "rcsb_uniprot_keyword": [
- {
- "id": "KW-0275, KW-0597\n",
- "value": "Lipid metabolism, Phosphoprotein, Fatty acid biosynthesis\n"
}
], - "rcsb_uniprot_protein": {
- "sequence": "string",
- "name": {
- "value": "Hemoglobin alpha\n",
- "provenance_code": "string"
}, - "function": {
- "details": "string",
- "provenance_code": "string"
}, - "gene": [
- {
- "name": [
- {
- "type": "PRIMARY",
- "value": "string"
}
]
}
], - "source_organism": {
- "scientific_name": "string",
- "taxonomy_id": 0,
- "provenance_code": "string"
}, - "ec": [
- {
- "number": "string",
- "provenance_code": "string"
}
]
}, - "rcsb_uniprot_feature": [
- {
- "assignment_version": "string",
- "description": "string",
- "feature_id": "string",
- "name": "string",
- "provenance_source": "string",
- "reference_scheme": "string",
- "type": "ACTIVE_SITE",
- "feature_positions": [
- {
- "beg_comp_id": "string",
- "beg_seq_id": 0,
- "end_seq_id": 0,
- "value": 0.1,
- "values": [
- 0.1
]
}
]
}
], - "rcsb_uniprot_annotation": [
- {
- "annotation_id": "string",
- "assignment_version": "string",
- "description": "string",
- "name": "string",
- "provenance_source": "string",
- "type": "disease",
- "annotation_lineage": [
- {
- "depth": 0,
- "id": "string",
- "name": "string"
}
], - "additional_properties": [
- {
- "name": "INTERPRO_TYPE\n",
- "values": [
- { }
]
}
]
}
], - "rcsb_uniprot_external_reference": [
- {
- "reference_id": "string",
- "reference_name": "IMPC",
- "provenance_source": "string"
}
], - "rcsb_uniprot_alignments": {
- "core_entity_alignments": [
- {
- "scores": {
- "target_coverage": 0,
- "query_coverage": 0,
- "target_length": 0,
- "query_length": 0
}, - "aligned_regions": [
- {
- "target_begin": 0,
- "query_begin": 0,
- "length": 0
}
], - "core_entity_identifiers": {
- "entry_id": "string",
- "entity_id": "string"
}
}
]
}
}
]
provides access to information about structures at the level of unique molecular instances (chains)
entry_id required | string Example: 1US2 ID of the entry that needs to be fetched. |
asym_id required | string Example: C ID of the instance (chain) that needs to be fetched. |
{- "pdbx_struct_special_symmetry": [
- {
- "PDB_model_num": 0,
- "auth_seq_id": "string",
- "id": 0,
- "label_asym_id": "string",
- "label_comp_id": "string"
}
], - "pdbx_vrpt_summary_entity_fit_to_map": [
- {
- "PDB_model_num": 0,
- "Q_score": 0.1,
- "average_residue_inclusion": 0.1
}
], - "pdbx_vrpt_summary_entity_geometry": [
- {
- "PDB_model_num": 0,
- "angles_RMSZ": 0.1,
- "average_residue_inclusion": 0.1,
- "bonds_RMSZ": 0.1,
- "num_angles_RMSZ": 0,
- "num_bonds_RMSZ": 0
}
], - "rcsb_ligand_neighbors": [
- {
- "alt_id": "string",
- "atom_id": "O1, N1, C1\n",
- "auth_seq_id": 0,
- "comp_id": "string",
- "distance": 0.1,
- "ligand_alt_id": "string",
- "ligand_asym_id": "A, B\n",
- "ligand_atom_id": "OG, OE1, CD1\n",
- "ligand_comp_id": "ASN, TRP, SER\n",
- "ligand_entity_id": "1, 2\n",
- "ligand_is_bound": "Y, N\n",
- "ligand_model_id": 0,
- "seq_id": 0
}
], - "rcsb_polymer_entity_instance_container_identifiers": {
- "asym_id": "string",
- "auth_asym_id": "string",
- "auth_to_entity_poly_seq_mapping": [
- "string"
], - "entity_id": "string",
- "entry_id": "string",
- "rcsb_id": "1KIP.A\n"
}, - "rcsb_polymer_instance_annotation": [
- {
- "annotation_id": "string",
- "assignment_version": "V4_0_2\n",
- "description": "string",
- "name": "string",
- "ordinal": 0,
- "provenance_source": "PDB\n",
- "type": "CATH, SCOP\n",
- "annotation_lineage": [
- {
- "depth": 0,
- "id": "string",
- "name": "string"
}
]
}
], - "rcsb_polymer_instance_feature": [
- {
- "assignment_version": "V4_0_2\n",
- "description": "string",
- "feature_id": "string",
- "name": "string",
- "ordinal": 0,
- "provenance_source": "CATH, SCOP\n",
- "reference_scheme": "PDB entity, UniProt, NCBI\n",
- "type": "CATH, SCOP\n",
- "feature_positions": [
- {
- "beg_comp_id": "TRP, VAL\n",
- "beg_seq_id": 0,
- "end_seq_id": 0,
- "value": 0.1,
- "values": [
- 0.1
]
}
], - "additional_properties": [
- {
- "name": "CATH_NAME, PARTNER_BOND_DISTANCE\n",
- "values": [
- { }
]
}
]
}
], - "rcsb_polymer_instance_feature_summary": [
- {
- "count": 0,
- "coverage": 0.1,
- "maximum_length": 0,
- "maximum_value": 0.1,
- "minimum_length": 0,
- "minimum_value": 0.1,
- "type": "CATH, SCOP\n"
}
], - "rcsb_polymer_struct_conn": [
- {
- "connect_type": "covalent bond",
- "description": "Watson-Crick base pair\n",
- "dist_value": 0.1,
- "id": "string",
- "ordinal_id": 0,
- "role": "N-Glycosylation, O-Glycosylation\n",
- "value_order": "doub",
- "connect_target": {
- "auth_asym_id": "string",
- "auth_seq_id": "string",
- "label_alt_id": "string",
- "label_asym_id": "string",
- "label_atom_id": "string",
- "label_comp_id": "string",
- "label_seq_id": 0,
- "symmetry": "1_555, 7_645\n"
}, - "connect_partner": {
- "label_alt_id": "string",
- "label_asym_id": "string",
- "label_atom_id": "string",
- "label_comp_id": "string",
- "label_seq_id": 0,
- "symmetry": "1_555, 7_645\n"
}
}
], - "struct_asym": {
- "pdbx_PDB_id": "1ABC\n",
- "pdbx_alt_id": "string",
- "pdbx_order": 0,
- "pdbx_type": "ATOMN"
}, - "rcsb_id": "1KIP.A\n",
- "rcsb_latest_revision": {
- "major_revision": 0,
- "minor_revision": 0,
- "revision_date": "2019-08-24T14:15:22Z"
}
}
entry_id required | string Example: 2FBW ENTRY ID of the entry. |
asym_id required | string Example: J ASYM ID (label_asym_id) of the instance (chain). |
{- "pdbx_struct_special_symmetry": [
- {
- "PDB_model_num": 0,
- "auth_seq_id": "string",
- "id": 0,
- "label_asym_id": "string",
- "label_comp_id": "string"
}
], - "pdbx_vrpt_summary_entity_fit_to_map": [
- {
- "PDB_model_num": 0,
- "Q_score": 0.1,
- "average_residue_inclusion": 0.1
}
], - "pdbx_vrpt_summary_entity_geometry": [
- {
- "PDB_model_num": 0,
- "angles_RMSZ": 0.1,
- "average_residue_inclusion": 0.1,
- "bonds_RMSZ": 0.1,
- "num_angles_RMSZ": 0,
- "num_bonds_RMSZ": 0
}
], - "rcsb_nonpolymer_entity_instance_container_identifiers": {
- "asym_id": "string",
- "auth_asym_id": "string",
- "auth_seq_id": "string",
- "comp_id": "string",
- "entity_id": "string",
- "entry_id": "string",
- "rcsb_id": "1KIP.A\n"
}, - "rcsb_nonpolymer_instance_annotation": [
- {
- "annotation_id": "string",
- "assignment_version": "V4_0_2\n",
- "comp_id": "ATP\n",
- "description": "string",
- "name": "string",
- "ordinal": 0,
- "provenance_source": "PDB\n",
- "type": "HAS_COVALENT_LINKAGE\n",
- "annotation_lineage": [
- {
- "depth": 0,
- "id": "string",
- "name": "string"
}
]
}
], - "rcsb_nonpolymer_instance_feature": [
- {
- "assignment_version": "V4_0_2\n",
- "comp_id": "string",
- "description": "string",
- "feature_id": "string",
- "name": "string",
- "ordinal": 0,
- "provenance_source": "PDB\n",
- "type": "RSRZ_OUTLIER, MOGUL_BOND_OUTLIER\n",
- "feature_value": [
- {
- "comp_id": "ATP,, STN\n",
- "details": "C1,C2, C1,C2,C3\n",
- "reference": 0.1,
- "reported": 0.1,
- "uncertainty_estimate": 0.1,
- "uncertainty_estimate_type": "Z-score\n"
}
], - "additional_properties": [
- {
- "name": "bond_distance, bond_angle\n",
- "values": [
- { }
]
}
]
}
], - "rcsb_nonpolymer_instance_feature_summary": [
- {
- "comp_id": "string",
- "count": 0,
- "coverage": 0.1,
- "maximum_length": 0,
- "maximum_value": 0.1,
- "minimum_length": 0,
- "minimum_value": 0.1,
- "type": "RSRZ_OUTLIER, MOGUL_BOND_OUTLIER\n"
}
], - "rcsb_nonpolymer_instance_validation_score": [
- {
- "RSCC": 0.1,
- "RSR": 0.1,
- "alt_id": "string",
- "average_occupancy": 0.1,
- "completeness": 0.1,
- "intermolecular_clashes": 0,
- "is_best_instance": "Y, N\n",
- "is_subject_of_investigation": "Y, N\n",
- "is_subject_of_investigation_provenance": "Author, RCSB\n",
- "mogul_angle_outliers": 0,
- "mogul_angles_RMSZ": 0.1,
- "mogul_bond_outliers": 0,
- "mogul_bonds_RMSZ": 0.1,
- "natoms_eds": 0,
- "num_mogul_angles_RMSZ": 0,
- "num_mogul_bonds_RMSZ": 0,
- "ranking_model_fit": 0.1,
- "ranking_model_geometry": 0.1,
- "score_model_fit": 0.1,
- "score_model_geometry": 0.1,
- "stereo_outliers": 0,
- "type": "RCSB_LIGAND_QUALITY_2021\n"
}
], - "rcsb_nonpolymer_struct_conn": [
- {
- "connect_type": "covalent bond",
- "description": "Watson-Crick base pair\n",
- "dist_value": 0.1,
- "id": "string",
- "ordinal_id": 0,
- "role": "N-Glycosylation, O-Glycosylation\n",
- "value_order": "doub",
- "connect_target": {
- "auth_asym_id": "string",
- "auth_seq_id": "string",
- "label_alt_id": "string",
- "label_asym_id": "string",
- "label_atom_id": "string",
- "label_comp_id": "string",
- "label_seq_id": 0,
- "symmetry": "1_555, 7_645\n"
}, - "connect_partner": {
- "label_alt_id": "string",
- "label_asym_id": "string",
- "label_atom_id": "string",
- "label_comp_id": "string",
- "label_seq_id": 0,
- "symmetry": "1_555, 7_645\n"
}
}
], - "rcsb_target_neighbors": [
- {
- "alt_id": "string",
- "atom_id": "O1, N1, C1\n",
- "comp_id": "string",
- "distance": 0.1,
- "target_asym_id": "A, B\n",
- "target_atom_id": "OG, OE1, CD1\n",
- "target_auth_seq_id": 0,
- "target_comp_id": "ASN, TRP, SER\n",
- "target_entity_id": "1, 2\n",
- "target_is_bound": "Y, N\n",
- "target_model_id": 0,
- "target_seq_id": 0
}
], - "struct_asym": {
- "pdbx_PDB_id": "1ABC\n",
- "pdbx_alt_id": "string",
- "pdbx_order": 0,
- "pdbx_type": "ATOMN"
}, - "rcsb_id": "1KIP.A\n",
- "rcsb_latest_revision": {
- "major_revision": 0,
- "minor_revision": 0,
- "revision_date": "2019-08-24T14:15:22Z"
}
}
entry_id required | string Example: 2FBW ENTRY ID of the entry. |
asym_id required | string Example: E ASYM ID (label_asym_id) of the instance (chain). |
{- "pdbx_struct_special_symmetry": [
- {
- "PDB_model_num": 0,
- "auth_seq_id": "string",
- "id": 0,
- "label_asym_id": "string",
- "label_comp_id": "string"
}
], - "pdbx_vrpt_summary_entity_fit_to_map": [
- {
- "PDB_model_num": 0,
- "Q_score": 0.1,
- "average_residue_inclusion": 0.1
}
], - "pdbx_vrpt_summary_entity_geometry": [
- {
- "PDB_model_num": 0,
- "angles_RMSZ": 0.1,
- "average_residue_inclusion": 0.1,
- "bonds_RMSZ": 0.1,
- "num_angles_RMSZ": 0,
- "num_bonds_RMSZ": 0
}
], - "rcsb_ligand_neighbors": [
- {
- "alt_id": "string",
- "atom_id": "O1, N1, C1\n",
- "auth_seq_id": 0,
- "comp_id": "string",
- "distance": 0.1,
- "ligand_alt_id": "string",
- "ligand_asym_id": "A, B\n",
- "ligand_atom_id": "OG, OE1, CD1\n",
- "ligand_comp_id": "ASN, TRP, SER\n",
- "ligand_entity_id": "1, 2\n",
- "ligand_is_bound": "Y, N\n",
- "ligand_model_id": 0,
- "seq_id": 0
}
], - "rcsb_polymer_entity_instance_container_identifiers": {
- "asym_id": "string",
- "auth_asym_id": "string",
- "auth_to_entity_poly_seq_mapping": [
- "string"
], - "entity_id": "string",
- "entry_id": "string",
- "rcsb_id": "1KIP.A\n"
}, - "rcsb_polymer_instance_annotation": [
- {
- "annotation_id": "string",
- "assignment_version": "V4_0_2\n",
- "description": "string",
- "name": "string",
- "ordinal": 0,
- "provenance_source": "PDB\n",
- "type": "CATH, SCOP\n",
- "annotation_lineage": [
- {
- "depth": 0,
- "id": "string",
- "name": "string"
}
]
}
], - "rcsb_polymer_instance_feature": [
- {
- "assignment_version": "V4_0_2\n",
- "description": "string",
- "feature_id": "string",
- "name": "string",
- "ordinal": 0,
- "provenance_source": "CATH, SCOP\n",
- "reference_scheme": "PDB entity, UniProt, NCBI\n",
- "type": "CATH, SCOP\n",
- "feature_positions": [
- {
- "beg_comp_id": "TRP, VAL\n",
- "beg_seq_id": 0,
- "end_seq_id": 0,
- "value": 0.1,
- "values": [
- 0.1
]
}
], - "additional_properties": [
- {
- "name": "CATH_NAME, PARTNER_BOND_DISTANCE\n",
- "values": [
- { }
]
}
]
}
], - "rcsb_polymer_instance_feature_summary": [
- {
- "count": 0,
- "coverage": 0.1,
- "maximum_length": 0,
- "maximum_value": 0.1,
- "minimum_length": 0,
- "minimum_value": 0.1,
- "type": "CATH, SCOP\n"
}
], - "rcsb_polymer_struct_conn": [
- {
- "connect_type": "covalent bond",
- "description": "Watson-Crick base pair\n",
- "dist_value": 0.1,
- "id": "string",
- "ordinal_id": 0,
- "role": "N-Glycosylation, O-Glycosylation\n",
- "value_order": "doub",
- "connect_target": {
- "auth_asym_id": "string",
- "auth_seq_id": "string",
- "label_alt_id": "string",
- "label_asym_id": "string",
- "label_atom_id": "string",
- "label_comp_id": "string",
- "label_seq_id": 0,
- "symmetry": "1_555, 7_645\n"
}, - "connect_partner": {
- "label_alt_id": "string",
- "label_asym_id": "string",
- "label_atom_id": "string",
- "label_comp_id": "string",
- "label_seq_id": 0,
- "symmetry": "1_555, 7_645\n"
}
}
], - "struct_asym": {
- "pdbx_PDB_id": "1ABC\n",
- "pdbx_alt_id": "string",
- "pdbx_order": 0,
- "pdbx_type": "ATOMN"
}, - "rcsb_id": "1KIP.A\n",
- "rcsb_latest_revision": {
- "major_revision": 0,
- "minor_revision": 0,
- "revision_date": "2019-08-24T14:15:22Z"
}
}
provides access to information about chemical components from which the relevant chemical structures can be constructed.
comp_id required | string Example: CFF CHEM COMP ID that uniquely identifies the chemical component. For protein polymer entities, this is the three-letter code for the amino acid. For nucleic acid polymer entities, this is the one-letter code for the base. |
{- "chem_comp": {
- "formula": "C18 H19 N7 O8 S\n",
- "formula_weight": 0.1,
- "id": "ALA, VAL, DG, C\n",
- "mon_nstd_parent_comp_id": [
- "string"
], - "name": "alanine, valine, adenine, cytosine\n",
- "one_letter_code": "A, B, R, N, D, C, Q, E, Z, G, H, I, L, K, M, F, P, S, T, W, Y, V, U, O, X\n",
- "pdbx_ambiguous_flag": "string",
- "pdbx_formal_charge": 0,
- "pdbx_initial_date": "2019-08-24T14:15:22Z",
- "pdbx_modified_date": "2019-08-24T14:15:22Z",
- "pdbx_processing_site": "EBI",
- "pdbx_release_status": "DEL",
- "pdbx_replaced_by": "q11, tvx\n",
- "pdbx_replaces": "q11, tvx,atv\n",
- "pdbx_subcomponent_list": "TSM DPH HIS CHF EMR\n",
- "three_letter_code": "ALA, ARG, ASN, ASP, ASX, CYS, GLN, GLU, GLY, GLX, HIS, ILE, LEU, LYS, MET, PHE, PRO, SER, THR, TRP, TYR, VAL, 1MA, 5MC, OMC, 1MG, 2MG, M2G, 7MG, 0MG, H2U, 5MU, PSU, ACE, FOR, HOH, UNK\n",
- "type": "D-beta-peptide, C-gamma linking"
}, - "pdbx_chem_comp_audit": [
- {
- "action_type": "Create component",
- "comp_id": "string",
- "date": "2019-08-24T14:15:22Z",
- "details": "Added C14 as a leaving atom.\n",
- "ordinal": 0
}
], - "pdbx_chem_comp_descriptor": [
- {
- "comp_id": "string",
- "descriptor": "string",
- "program": "OPENEYE, CACTVS, DAYLIGHT, OTHER\n",
- "program_version": "string",
- "type": "InChI"
}
], - "pdbx_chem_comp_feature": [
- {
- "comp_id": "ABC, ATP\n",
- "source": "PDB, CHEBI, DRUGBANK, PUBCHEM\n",
- "type": "CARBOHYDRATE ANOMER, CARBOHYDRATE ISOMER, CARBOHYDRATE RING\n",
- "value": "string"
}
], - "pdbx_chem_comp_identifier": [
- {
- "comp_id": "string",
- "identifier": "string",
- "program": "OPENEYE, DAYLIGHT, ACD, AUTONOM, PUBCHEM_CID, PUBCHEM_SID, OTHER, NONE\n",
- "program_version": "string",
- "type": "CAS REGISTRY NUMBER"
}
], - "pdbx_family_prd_audit": [
- {
- "action_type": "Add PRD",
- "annotator": "JO, SJ, KB\n",
- "date": "2019-08-24T14:15:22Z",
- "details": "Revise molecule sequence.\n",
- "family_prd_id": "string",
- "processing_site": "RCSB, PDBE, PDBJ, BMRB, PDBC\n"
}
], - "pdbx_prd_audit": [
- {
- "action_type": "Create molecule",
- "annotator": "JO, SJ, KB\n",
- "date": "2019-08-24T14:15:22Z",
- "details": "Revise molecule sequence.\n",
- "prd_id": "string",
- "processing_site": "RCSB, PDBE, PDBJ, BMRB, PDBC\n"
}
], - "pdbx_reference_entity_list": [
- {
- "component_id": 0,
- "details": "string",
- "prd_id": "string",
- "ref_entity_id": "string",
- "type": "polymer, non-polymer, branched\n"
}
], - "pdbx_reference_entity_poly": [
- {
- "db_code": "string",
- "db_name": "string",
- "prd_id": "string",
- "ref_entity_id": "string",
- "type": "peptide-like\n"
}
], - "pdbx_reference_entity_poly_link": [
- {
- "atom_id_1": "string",
- "atom_id_2": "string",
- "comp_id_1": "string",
- "comp_id_2": "string",
- "component_id": 0,
- "entity_seq_num_1": 0,
- "entity_seq_num_2": 0,
- "link_id": 0,
- "prd_id": "string",
- "ref_entity_id": "string",
- "value_order": "arom"
}
], - "pdbx_reference_entity_poly_seq": [
- {
- "hetero": "N\n",
- "mon_id": "string",
- "num": 0,
- "observed": "Y\n",
- "parent_mon_id": "string",
- "prd_id": "string",
- "ref_entity_id": "string"
}
], - "pdbx_reference_entity_sequence": [
- {
- "NRP_flag": "Y\n",
- "one_letter_codes": "string",
- "prd_id": "string",
- "ref_entity_id": "string",
- "type": "peptide-like, saccharide\n"
}
], - "pdbx_reference_entity_src_nat": [
- {
- "atcc": "string",
- "db_code": "string",
- "db_name": "string",
- "ordinal": 0,
- "organism_scientific": "Mus musculus\n",
- "prd_id": "string",
- "ref_entity_id": "string",
- "source": "string",
- "source_id": "string",
- "taxid": "string"
}
], - "pdbx_reference_molecule": {
- "chem_comp_id": "0Z3, CD9\n",
- "class": "Antagonist",
- "class_evidence_code": "string",
- "compound_details": "string",
- "description": "string",
- "formula": "C18 H19 N7 O8 S\n",
- "formula_weight": 0.1,
- "name": "thiostrepton\n",
- "prd_id": "PRD_000001, PRD_0000010\n",
- "release_status": "HOLD",
- "replaced_by": "string",
- "replaces": "string",
- "represent_as": "branched",
- "representative_PDB_id_code": "string",
- "type": "Peptide-like, Macrolide\n",
- "type_evidence_code": "string"
}, - "pdbx_reference_molecule_annotation": [
- {
- "family_prd_id": "string",
- "ordinal": 0,
- "prd_id": "string",
- "source": "depositor provided, from UniProt Entry P200311\n",
- "text": "antigen binding, glucose transporter activity\n",
- "type": "Function, Use, Pharmacology, Mechanism_of_Action, Biological_Activity, Inhibitor_Class, Therapeutic_Category, Research_Use, Other_annotation\n"
}
], - "pdbx_reference_molecule_details": [
- {
- "family_prd_id": "string",
- "ordinal": 0,
- "source": "string",
- "source_id": "string",
- "text": "string"
}
], - "pdbx_reference_molecule_family": {
- "family_prd_id": "string",
- "name": "actinomycin, adriamycin\n",
- "release_status": "HOLD",
- "replaced_by": "string",
- "replaces": "string"
}, - "pdbx_reference_molecule_features": [
- {
- "family_prd_id": "string",
- "ordinal": 0,
- "prd_id": "string",
- "source": "PDB, CHEBI, DRUGBANK, PUBCHEM\n",
- "source_ordinal": 0,
- "type": "FUNCTION, ENZYME INHIBITED, STRUCTURE IMAGE URL\n",
- "value": "string"
}
], - "pdbx_reference_molecule_list": [
- {
- "family_prd_id": "string",
- "prd_id": "string"
}
], - "pdbx_reference_molecule_related_structures": [
- {
- "citation_id": "string",
- "db_accession": "143108",
- "db_code": "QEFHUE\n",
- "db_name": "CCDC\n",
- "family_prd_id": "string",
- "formula": "C18 H19 N7 O8 S\n",
- "name": "actinomycn\n",
- "ordinal": 0
}
], - "pdbx_reference_molecule_synonyms": [
- {
- "family_prd_id": "string",
- "name": "thiostrepton\n",
- "ordinal": 0,
- "prd_id": "string",
- "source": "CAS\n"
}
], - "rcsb_bird_citation": [
- {
- "id": "1, 2\n",
- "journal_abbrev": "J.Mol.Biol., J. Mol. Biol.\n",
- "journal_volume": "174",
- "page_first": "string",
- "page_last": "string",
- "pdbx_database_id_DOI": "10.2345/S1384107697000225\n",
- "pdbx_database_id_PubMed": 0,
- "rcsb_authors": [
- "string"
], - "title": "Structure of diferric duck ovotransferrin\n at 2.35 Angstroms resolution.\n",
- "year": 0
}
], - "rcsb_chem_comp_annotation": [
- {
- "annotation_id": "string",
- "assignment_version": "V4_0_2\n",
- "description": "string",
- "name": "string",
- "provenance_source": "RESID, UniProt, PDB\n",
- "type": "PSI-MOD\n",
- "annotation_lineage": [
- {
- "depth": 0,
- "id": "string",
- "name": "string"
}
]
}
], - "rcsb_chem_comp_container_identifiers": {
- "atc_codes": [
- "string"
], - "comp_id": "ATP, STI\n",
- "drugbank_id": "DB00781, DB15263\n",
- "prd_id": "PRD_000010\n",
- "rcsb_id": "ATP, PRD_000010\n",
- "subcomponent_ids": [
- "string"
]
}, - "rcsb_chem_comp_descriptor": {
- "InChI": "InChI=1S/C3H6FO6P/c4-1-2(3(5)6)10-11(7,8)9/h2H,1H2,(H,5,6)(H2,7,8,9)/t2-/m0/s1\n",
- "InChIKey": "BNOCDEBUFVJMQI-REOHCLBHSA-N\n",
- "SMILES": "OC(=O)[CH](CF)O[P](O)(O)=O\n",
- "SMILES_stereo": "OC(=O)[C@H](CF)O[P](O)(O)=O\n",
- "comp_id": "string"
}, - "rcsb_chem_comp_info": {
- "atom_count": 0,
- "atom_count_chiral": 0,
- "atom_count_heavy": 0,
- "bond_count": 0,
- "bond_count_aromatic": 0,
- "comp_id": "string",
- "initial_deposition_date": "2019-08-24T14:15:22Z",
- "initial_release_date": "2019-08-24T14:15:22Z",
- "release_status": "REL\n",
- "revision_date": "2019-08-24T14:15:22Z"
}, - "rcsb_chem_comp_related": [
- {
- "comp_id": "string",
- "ordinal": 0,
- "related_mapping_method": "assigned by DrugBank resource\n",
- "resource_accession_code": "124832",
- "resource_name": "CCDC/CSD\n"
}
], - "rcsb_chem_comp_synonyms": [
- {
- "comp_id": "string",
- "name": "Ursonic acid, Talotrexin, 4-oxodecanedioic acid\n",
- "ordinal": 0,
- "provenance_source": "ACDLabs",
- "type": "Brand Name"
}
], - "rcsb_chem_comp_target": [
- {
- "comp_id": "string",
- "interaction_type": "string",
- "name": "string",
- "ordinal": 0,
- "provenance_source": "DrugBank",
- "reference_database_accession_code": "Q9HD40\n",
- "reference_database_name": "UniProt\n",
- "target_actions": [
- "string"
]
}
], - "rcsb_schema_container_identifiers": [
- {
- "collection_name": "string",
- "collection_schema_version": "string",
- "schema_name": "string"
}
], - "rcsb_id": "ATP, PRD_000010\n"
}
comp_id required | string Example: CFF CHEM COMP ID that uniquely identifies the chemical component. For protein polymer entities, this is the three-letter code for the amino acid. For nucleic acid polymer entities, this is the one-letter code for the base. |
{- "drugbank_container_identifiers": {
- "drugbank_id": "string"
}, - "drugbank_info": {
- "affected_organisms": [
- "string"
], - "atc_codes": [
- "string"
], - "brand_names": [
- "string"
], - "cas_number": "56-65-5\n",
- "description": "string",
- "drug_categories": [
- "string"
], - "drug_groups": "approved",
- "drugbank_id": "string",
- "indication": "For nutritional supplementation, also for treating dietary shortage or imbalance\n",
- "mechanism_of_action": "ATP is able to store and transport chemical energy within cells.\n",
- "name": "string",
- "pharmacology": "Adenosine triphosphate (ATP) is the nucleotide known in biochemistry as the \"molecular currency\" of intracellular energy transfer; that is, ATP is able to store and transport chemical energy within cells. ATP also plays an important role in the synthesis of nucleic acids. The total quantity of ATP in the human body is about 0.1 mole. The energy used by human cells requires the hydrolysis of 200 to 300 moles of ATP daily. This means that each ATP molecule is recycled 2000 to 3000 times during a single day. ATP cannot be stored, hence its consumption must closely follow its synthesis.\n",
- "synonyms": [
- "string"
], - "drug_products": [
- {
- "approved": "N",
- "country": "Canada\n",
- "ended_marketing_on": "2019-08-24T14:15:22Z",
- "name": "Hivid Tab 0.375mg\n",
- "source": "DPD\n",
- "started_marketing_on": "2019-08-24T14:15:22Z"
}
]
}, - "drugbank_target": [
- {
- "interaction_type": "string",
- "name": "string",
- "ordinal": 0,
- "organism_common_name": "string",
- "reference_database_accession_code": "Q9HD40\n",
- "reference_database_name": "UniProt\n",
- "seq_one_letter_code": "MAKQRSG...\n",
- "target_actions": [
- "string"
]
}
]
}
entry_id required | string Example: 4ACQ ENTRY ID of the entry. |
{- "audit_author": [
- {
- "identifier_ORCID": "0000-0002-6681-547X\n",
- "name": "Jones, T.J., Bleary, Percival R., O'Neil, F.K., Van den Bossche, G., Yang, D.-L., Simonov, Yu.A\n",
- "pdbx_ordinal": 0
}
], - "cell": {
- "Z_PDB": 0,
- "angle_alpha": 0.1,
- "angle_beta": 0.1,
- "angle_gamma": 0.1,
- "formula_units_Z": 0,
- "length_a": 0.1,
- "length_b": 0.1,
- "length_c": 0.1,
- "pdbx_unique_axis": "string",
- "volume": 0.1
}, - "citation": [
- {
- "book_id_ISBN": "string",
- "book_publisher": "John Wiley and Sons\n",
- "book_publisher_city": "London\n",
- "book_title": "string",
- "coordinate_linkage": "n",
- "country": "string",
- "id": "primary, 1, 2\n",
- "journal_abbrev": "J.Mol.Biol., J. Mol. Biol.\n",
- "journal_full": "Journal of Molecular Biology\n",
- "journal_id_ASTM": "string",
- "journal_id_CSD": "0070\n",
- "journal_id_ISSN": "string",
- "journal_issue": "2",
- "journal_volume": "174",
- "language": "German\n",
- "page_first": "string",
- "page_last": "string",
- "pdbx_database_id_DOI": "10.2345/S1384107697000225\n",
- "pdbx_database_id_PubMed": 0,
- "rcsb_authors": [
- "string"
], - "rcsb_is_primary": "Y\n",
- "rcsb_journal_abbrev": "Nat Struct Mol Biol\n",
- "title": "Structure of diferric duck ovotransferrin\n at 2.35 Angstroms resolution.\n",
- "unpublished_flag": "N",
- "year": 0
}
], - "diffrn": [
- {
- "ambient_pressure": 0.1,
- "ambient_temp": 0.1,
- "ambient_temp_details": "string",
- "crystal_id": "string",
- "crystal_support": "glass capillary, quartz capillary, fiber, metal loop\n",
- "details": "string",
- "id": "string",
- "pdbx_serial_crystal_experiment": "Y, N\n"
}
], - "diffrn_detector": [
- {
- "details": "string",
- "detector": "photographic film, scintillation counter, CCD plate, BF~3~ counter\n",
- "diffrn_id": "string",
- "pdbx_collection_date": "2019-08-24T14:15:22Z",
- "pdbx_frequency": 0.1,
- "type": "DECTRIS PILATUS 12M, RAYONIX MX-325\n"
}
], - "diffrn_radiation": [
- {
- "collimation": "0.3 mm double-pinhole, 0.5 mm, focusing mirrors\n",
- "diffrn_id": "string",
- "monochromator": "Zr filter, Ge 220, none, equatorial mounted graphite\n",
- "pdbx_diffrn_protocol": "SINGLE WAVELENGTH, MONOCHROMATIC, LAUE, MAD, OTHER\n",
- "pdbx_monochromatic_or_laue_m_l": "M, L\n",
- "pdbx_scattering_type": "electron",
- "pdbx_wavelength": "string",
- "pdbx_wavelength_list": "string",
- "type": "CuK\\a, Cu K\\a~1~, Cu K-L~2,3~, white-beam\n",
- "wavelength_id": "string"
}
], - "diffrn_source": [
- {
- "details": "string",
- "diffrn_id": "string",
- "pdbx_synchrotron_beamline": "17-ID-1, 19-ID\n",
- "pdbx_synchrotron_site": "APS, NSLS-II\n",
- "pdbx_wavelength": "string",
- "pdbx_wavelength_list": "0.987 or 0.987, 0.988, 1.0 or 0.99-1.5\n",
- "source": "sealed X-ray tube, nuclear reactor, spallation source, electron microscope, rotating-anode X-ray tube, synchrotron\n",
- "type": "NSLS beamline X8C, Rigaku RU200\n"
}
], - "em_2d_crystal_entity": [
- {
- "angle_gamma": 0.1,
- "c_sampling_length": 0.1,
- "id": "string",
- "image_processing_id": "string",
- "length_a": 0.1,
- "length_b": 0.1,
- "length_c": 0.1,
- "space_group_name_H_M": "C 1 2"
}
], - "em_3d_crystal_entity": [
- {
- "angle_alpha": 0.1,
- "angle_beta": 0.1,
- "angle_gamma": 0.1,
- "id": "string",
- "image_processing_id": "string",
- "length_a": 0.1,
- "length_b": 0.1,
- "length_c": 0.1,
- "space_group_name": "P 1, P 21 21 2, I 4, H 3\n",
- "space_group_num": 0
}
], - "em_3d_fitting": [
- {
- "details": "Initial local fitting was done using Chimera and then NMFF was used for flexible fitting.\n",
- "id": "string",
- "method": "string",
- "overall_b_value": 0.1,
- "ref_protocol": "AB INITIO MODEL",
- "ref_space": "REAL",
- "target_criteria": "Cross-correlation coefficient\n"
}
], - "em_3d_fitting_list": [
- {
- "3d_fitting_id": "string",
- "details": "The initial model consisted of the complete biological assembly for PDB entry 2GTL.\n",
- "id": "string",
- "pdb_chain_id": "The ID of the biopolymer chain used for fitting, e.g., A. Please note that only one chain can be specified per instance. If all chains of a particular structure have been used for fitting, this field can be left blank.\n",
- "pdb_chain_residue_range": "string",
- "pdb_entry_id": "1EHZ\n"
}
], - "em_3d_reconstruction": [
- {
- "actual_pixel_size": 0.1,
- "algorithm": "string",
- "details": "a modified version of SPIDER program was used for the reconstruction\n",
- "id": "string",
- "image_processing_id": "string",
- "magnification_calibration": "TMV images\n",
- "method": "cross-common lines, polar Fourier transform (PFT)\n",
- "nominal_pixel_size": 0.1,
- "num_class_averages": 0,
- "num_particles": 0,
- "refinement_type": "HALF-MAPS REFINED AGAINST SAME DATA",
- "resolution": 0.1,
- "resolution_method": "FSC at 0.5 cut-off\n",
- "symmetry_type": "2D CRYSTAL"
}
], - "em_ctf_correction": [
- {
- "details": "CTF amplitude correction was performed following 3D reconstruction\n",
- "em_image_processing_id": "string",
- "id": "string",
- "type": "string"
}
], - "em_diffraction": [
- {
- "camera_length": 0.1,
- "id": "string",
- "imaging_id": "string",
- "tilt_angle_list": "20,40,50,55\n"
}
], - "em_diffraction_shell": [
- {
- "em_diffraction_stats_id": "string",
- "fourier_space_coverage": 0.1,
- "high_resolution": 0.1,
- "id": "string",
- "low_resolution": 0.1,
- "multiplicity": 0.1,
- "num_structure_factors": 0,
- "phase_residual": 0.1
}
], - "em_diffraction_stats": [
- {
- "details": "Phases were obtained from micrograph images of the 2D crystals\n",
- "fourier_space_coverage": 0.1,
- "high_resolution": 0.1,
- "id": "string",
- "image_processing_id": "string",
- "num_intensities_measured": 0,
- "num_structure_factors": 0,
- "overall_phase_error": 0.1,
- "overall_phase_residual": 0.1,
- "phase_error_rejection_criteria": "Structure factors with phase errors higher than 20 degrees were omitted from refinement\n",
- "r_merge": 0.1,
- "r_sym": 0.1
}
], - "em_embedding": [
- {
- "details": "The crystal suspension was injected into the lens of a drop of buffer containing\n 1 % tannin sitting on a carbon film supported by a molybdenum grid. An equal volume\n of 1% glucose was then added and the solution thoroughly but gently mixed. The grid\n was then blotted, air dried, and frozen in LN2.\n",
- "id": "string",
- "material": "tannin and glucose\n",
- "specimen_id": "string"
}
], - "em_entity_assembly": [
- {
- "details": "Fab fragment generated by proteolytic cleavage of LA2 IgG antibody.\n",
- "entity_id_list": [
- "string"
], - "id": "string",
- "name": "Ternary complex of alpha-tubulin with tubulin folding cofactors TBCE and TBCB, 80S Ribosome bound to emetine, messenger RNA, initiation factor 2, GroEL, antibody Fab fragment\n",
- "oligomeric_details": "string",
- "parent_id": 0,
- "source": "MULTIPLE SOURCES",
- "synonym": "FADV-1\n",
- "type": "string"
}
], - "em_experiment": {
- "aggregation_state": "2D ARRAY",
- "entity_assembly_id": "string",
- "id": "string",
- "reconstruction_method": "CRYSTALLOGRAPHY"
}, - "em_helical_entity": [
- {
- "angular_rotation_per_subunit": 0.1,
- "axial_rise_per_subunit": 0.1,
- "axial_symmetry": "C1, D2, C7\n",
- "details": "Dihedral symmetry\n",
- "id": "string",
- "image_processing_id": "string"
}
], - "em_image_recording": [
- {
- "average_exposure_time": 0.1,
- "avg_electron_dose_per_image": 0.1,
- "details": "Images were collected in movie-mode at 17 frames per second\n",
- "detector_mode": "COUNTING",
- "film_or_detector_model": "string",
- "id": "string",
- "imaging_id": "string",
- "num_diffraction_images": 0,
- "num_grids_imaged": 0,
- "num_real_images": 0
}
], - "em_imaging": [
- {
- "accelerating_voltage": 0,
- "alignment_procedure": "BASIC",
- "astigmatism": "string",
- "c2_aperture_diameter": 0.1,
- "calibrated_defocus_max": 0.1,
- "calibrated_defocus_min": 0.1,
- "calibrated_magnification": 0,
- "cryogen": "HELIUM",
- "date": "2019-08-24T14:15:22Z",
- "details": "Preliminary grid screening was performed manually.\n",
- "detector_distance": 0.1,
- "electron_beam_tilt_params": "string",
- "electron_source": "string",
- "id": "string",
- "illumination_mode": "FLOOD BEAM",
- "microscope_model": "FEI MORGAGNI",
- "mode": "4D-STEM",
- "nominal_cs": 0.1,
- "nominal_defocus_max": 0.1,
- "nominal_defocus_min": 0.1,
- "nominal_magnification": 0,
- "recording_temperature_maximum": 0.1,
- "recording_temperature_minimum": 0.1,
- "residual_tilt": 0.1,
- "specimen_holder_model": "FEI TITAN KRIOS AUTOGRID HOLDER",
- "specimen_holder_type": "cryo\n",
- "specimen_id": "string",
- "temperature": 0.1,
- "tilt_angle_max": 0.1,
- "tilt_angle_min": 0.1
}
], - "em_particle_selection": [
- {
- "details": "negative monitor contrast facilitated particle picking\n",
- "id": "string",
- "image_processing_id": "string",
- "num_particles_selected": 0
}
], - "em_single_particle_entity": [
- {
- "id": 0,
- "image_processing_id": "string",
- "point_symmetry": "C1, C5, C4\n"
}
], - "em_software": [
- {
- "category": "CLASSIFICATION",
- "details": "EMAN2 e2boxer.py was used to automatically select particle images.\n",
- "fitting_id": "string",
- "id": "string",
- "image_processing_id": "string",
- "imaging_id": "string",
- "name": "EMAN, Imagic, Spider, Bsoft, UCSF-Chimera\n",
- "version": "9.03, 2.1\n"
}
], - "em_specimen": [
- {
- "concentration": 0.1,
- "details": "This sample was monodisperse., Au was deposited at a 30 degree angle to 15 nm thickness., Colloidal gold particles were deposited by dipping into dilute solution., The specimen was frozen at high pressure using the bal-tec hpm 010 instrument., The embedded sample was sectioned at 100 K to 50 nm final thickness.\n",
- "embedding_applied": "NO",
- "experiment_id": "string",
- "id": "string",
- "shadowing_applied": "NO",
- "staining_applied": "NO",
- "vitrification_applied": "NO"
}
], - "em_staining": [
- {
- "details": "Negatively stained EM specimens were prepared using a carbon-sandwich technique\n and uranyl-formate stain.\n",
- "id": "string",
- "material": "Uranyl Acetate\n",
- "specimen_id": "string",
- "type": "NEGATIVE"
}
], - "em_vitrification": [
- {
- "chamber_temperature": 0.1,
- "cryogen_name": "ETHANE",
- "details": "Vitrification carried out in argon atmosphere.\n",
- "humidity": 0.1,
- "id": "string",
- "instrument": "CRYOSOL VITROJET",
- "method": "plunge freezing\n",
- "specimen_id": "string",
- "temp": 0.1,
- "time_resolved_state": "plunge 30 msec after spraying with effector\n"
}
], - "entry": {
- "id": "string",
- "ma_collection_id": "string"
}, - "exptl": [
- {
- "crystals_number": 0,
- "details": "string",
- "method": "X-RAY DIFFRACTION, NEUTRON DIFFRACTION, FIBER DIFFRACTION, ELECTRON CRYSTALLOGRAPHY, ELECTRON MICROSCOPY, SOLUTION NMR, SOLID-STATE NMR, SOLUTION SCATTERING, POWDER DIFFRACTION\n",
- "method_details": "29 structures, minimized average structure\n"
}
], - "exptl_crystal": [
- {
- "colour": "dark green\n",
- "density_Matthews": 0.1,
- "density_meas": 0.1,
- "density_percent_sol": 0.1,
- "description": "string",
- "id": "string",
- "pdbx_mosaicity": 0.1,
- "pdbx_mosaicity_esd": 0.1,
- "preparation": "mounted in an argon-filled quartz capillary\n"
}
], - "exptl_crystal_grow": [
- {
- "crystal_id": "string",
- "details": "Solution 2 was prepared as a well solution and\n mixed. A droplet containing 2 \\ml of solution\n 1 was delivered onto a cover slip; 2 \\ml of\n solution 2 was added to the droplet without\n mixing., Crystal plates were originally stored at room\n temperature for 1 week but no nucleation\n occurred. They were then transferred to 4\n degrees C, at which temperature well formed\n single crystals grew in 2 days., The dependence on pH for successful crystal\n growth is very sharp. At pH 7.4 only showers\n of tiny crystals grew, at pH 7.5 well formed\n single crystals grew, at pH 7.6 no\n crystallization occurred at all.\n",
- "method": "MICROBATCH, VAPOR DIFFUSION, HANGING DROP\n",
- "pH": 0.1,
- "pdbx_details": "PEG 4000, potassium phosphate, magnesium chloride, cacodylate\n",
- "pdbx_pH_range": "5.6 - 6.4\n",
- "temp": 0.1,
- "temp_details": "string"
}
], - "ma_data": [
- {
- "content_type": "coevolution MSA",
- "content_type_other_details": "string",
- "id": 0,
- "name": "NMR NOE Distances, Target Template Alignment, Coevolution Data\n"
}
], - "pdbx_SG_project": [
- {
- "full_name_of_center": "Midwest Center for Structural Genomics\n",
- "id": 1,
- "initial_of_center": "JCSG\n",
- "project_name": "PSI, Protein Structure Initiative\n"
}
], - "pdbx_audit_revision_category": [
- {
- "category": "audit_author, citation\n",
- "data_content_type": "Structure model\n",
- "ordinal": 0,
- "revision_ordinal": 0
}
], - "pdbx_audit_revision_details": [
- {
- "data_content_type": "Structure model\n",
- "description": "string",
- "details": "string",
- "ordinal": 0,
- "provider": "repository\n",
- "revision_ordinal": 0,
- "type": "Initial release\n"
}
], - "pdbx_audit_revision_group": [
- {
- "data_content_type": "Structure model\n",
- "group": "citation\n",
- "ordinal": 0,
- "revision_ordinal": 0
}
], - "pdbx_audit_revision_history": [
- {
- "data_content_type": "Structure model\n",
- "major_revision": 0,
- "minor_revision": 0,
- "ordinal": 0,
- "revision_date": "2019-08-24T14:15:22Z"
}
], - "pdbx_audit_revision_item": [
- {
- "data_content_type": "Structure model\n",
- "item": "_atom_site.type_symbol\n",
- "ordinal": 0,
- "revision_ordinal": 0
}
], - "pdbx_audit_support": [
- {
- "country": "string",
- "funding_organization": "National Institutes of Health, Wellcome Trust, National Institutes of Health/National Institute of General Medical Sciences\n",
- "grant_number": "string",
- "ordinal": 0
}
], - "pdbx_database_PDB_obs_spr": [
- {
- "date": "2019-08-24T14:15:22Z",
- "details": "string",
- "id": "OBSLTE\n",
- "pdb_id": "2ABC\n",
- "replace_pdb_id": "3ABC\n"
}
], - "pdbx_database_related": [
- {
- "content_type": "minimized average structure, representative structure, ensemble, derivative structure, native structure, associated EM volume, other EM volume, associated NMR restraints, associated structure factors, associated SAS data, protein target sequence and/or protocol data, split, re-refinement, complete structure, unspecified, other\n",
- "db_id": "1ABC, BDL001\n",
- "db_name": "PDB - Protein Databank\nNDB - Nucleic Acid Database\nBMRB - BioMagResBank\nEMDB - Electron Microscopy Database\nBMCD - Biological Macromolecule Crystallization Database\nTargetTrack - Target Registration and Protocol Database\nSASBDB - Small Angle Scattering Biological Data Bank\n",
- "details": "1ABC contains the same protein complexed with Netropsin.\n"
}
], - "pdbx_database_status": {
- "SG_entry": "Y\n",
- "deposit_site": "NDB, RCSB, PDBE, PDBJ, BMRB, BNL, PDBC\n",
- "methods_development_category": "CASP, CASD-NMR\n",
- "pdb_format_compatible": "Y\n",
- "process_site": "NDB, RCSB, PDBE, PDBJ, BNL, PDBC\n",
- "recvd_initial_deposition_date": "2019-08-24T14:15:22Z",
- "status_code": "REL, HPUB\n",
- "status_code_cs": "PROC = Processing in progress\n WAIT = Awaiting author approval\n REL = Release\n HOLD = On hold until yyyy-mm-dd\n HPUB = On hold until publication\n OBS = Entry has been obsoleted\n WDRN = Entry has been withdrawn by depositor\n",
- "status_code_mr": "PROC = To be processed\n REL = Release\n HOLD = On hold until yyyy-mm-dd\n HPUB = On hold until publication\n OBS = Entry has been obsoleted\n WDRN = Entry has been withdrawn by depositor\n WAIT = Awaiting author approval\n",
- "status_code_sf": "PROC = To be processed\n REL = Released\n HOLD = On hold until yyyy-mm-dd\n HPUB = On hold until publication\n OBS = Entry has been obsoleted\n WDRN = Entry has been withdrawn by depositor\n WAIT = Awaiting author approval\n"
}, - "pdbx_deposit_group": [
- {
- "group_description": "string",
- "group_id": "G_1002119, G_1002043\n",
- "group_title": "string",
- "group_type": "changed state"
}
], - "pdbx_initial_refinement_model": [
- {
- "accession_code": "string",
- "details": "string",
- "entity_id_list": [
- "string"
], - "id": 0,
- "source_name": "AlphaFold",
- "type": "experimental model"
}
], - "pdbx_molecule_features": [
- {
- "class": "Antagonist",
- "details": "string",
- "name": "thiostrepton\n",
- "prd_id": "string",
- "type": "Peptide-like, Macrolide\n"
}
], - "pdbx_nmr_details": {
- "text": "This structure was determined using standard 2D homonuclear techniques., The structure was determined using triple-resonance NMR spectroscopy.\n"
}, - "pdbx_nmr_ensemble": {
- "average_constraint_violations_per_residue": 0,
- "average_constraints_per_residue": 0,
- "average_distance_constraint_violation": 0.1,
- "average_torsion_angle_constraint_violation": 0.1,
- "conformer_selection_criteria": "structures with the lowest energy, structures with the least restraint violations, structures with acceptable covalent geometry, structures with favorable non-bond energy, target function, back calculated data agree with experimental NOESY spectrum, all calculated structures submitted, The submitted conformer models are the 25 structures with the lowest\n energy., The submitted conformer models are those with the fewest number of\n constraint violations.\n",
- "conformers_calculated_total_number": 0,
- "conformers_submitted_total_number": 0,
- "distance_constraint_violation_method": "Statistics were calculated over all of the distance constraints., Statistics were calculated for violations only\n",
- "maximum_distance_constraint_violation": 0.1,
- "maximum_lower_distance_constraint_violation": 0.1,
- "maximum_torsion_angle_constraint_violation": 0.1,
- "maximum_upper_distance_constraint_violation": 0.1,
- "representative_conformer": 0,
- "torsion_angle_constraint_violation_method": "Statistics were calculated over all the torsion angle constraints., Statistics were calculated for torsion angle constraints violations only.\n"
}, - "pdbx_nmr_exptl": [
- {
- "conditions_id": "1, 2, 3\n",
- "experiment_id": "1, 2, 3\n",
- "sample_state": "isotropic\n",
- "solution_id": "1, 2, 3\n",
- "spectrometer_id": 0,
- "type": "2D NOESY, 3D_15N-separated_NOESY, 3D_13C-separated_NOESY, 4D_13C-separated_NOESY, 4D_13C/15N-separated_NOESY, 3D_15N-separated_ROESY, 3D_13C-separated_ROESY, HNCA-J, HNHA, DQF-COSY, P-COSY, PE-COSY, E-COSY\n"
}
], - "pdbx_nmr_exptl_sample_conditions": [
- {
- "conditions_id": "1, 2, 3\n",
- "details": "The high salinity of the sample may have contributed to overheating of the sample during experiments with long saturation periods like the TOCSY experiments.\n",
- "ionic_strength": "string",
- "ionic_strength_err": 0.1,
- "ionic_strength_units": "M\n",
- "label": "conditions_1\n",
- "pH": "null, null\n",
- "pH_err": 0.1,
- "pH_units": "pH\n",
- "pressure": "1, ambient, 1atm\n",
- "pressure_err": 0.1,
- "pressure_units": "Pa, atm, Torr\n",
- "temperature": "string",
- "temperature_err": 0.1,
- "temperature_units": "K\n"
}
], - "pdbx_nmr_refine": [
- {
- "details": "Additional comments about the NMR refinement can be placed here, e.g.\nthe structures are based on a total of 3344 restraints, 3167 are NOE-derived\ndistance constraints, 68 dihedral angle restraints,109 distance restraints\nfrom hydrogen bonds.\n",
- "method": "simulated annealing, distance geometry\n simulated annealing\n molecular dynamics\n matrix relaxation\n torsion angle dynamics\n",
- "software_ordinal": 0
}
], - "pdbx_nmr_representative": {
- "conformer_id": "15",
- "selection_criteria": "The structure closest to the average.\nThe structure with the lowest energy was selected.\nThe structure with the fewest number of violations was selected.\nA minimized average structure was calculated.\n"
}, - "pdbx_nmr_sample_details": [
- {
- "contents": "2mM Ribonuclease U-15N,13C; 50mM phosphate buffer NA; 90% H2O, 10% D2O\n",
- "details": "The added glycerol was used to raise the viscosity of the solution to 1.05 poisson.\n",
- "label": "15N_sample\n",
- "solution_id": "1, 2, 3\n",
- "solvent_system": "90% H2O, 10% D2O\n",
- "type": "bicelle\n"
}
], - "pdbx_nmr_software": [
- {
- "authors": "Brunger, Guentert\n",
- "classification": "collection, processing, data analysis, structure solution, refinement, iterative matrix relaxation\n",
- "name": "ANSIG, AURELIA, AZARA, CHARMM, CoMAND, CORMA, DIANA, DYANA, DSPACE, DISGEO, DGII, DISMAN, DINOSAUR, DISCOVER, FELIX, FT_NMR, GROMOS, IRMA, MARDIGRAS, NMRPipe, SA, UXNMR, VNMR, X-PLOR, XWINNMR\n",
- "ordinal": 0,
- "version": "940501.3, 2.1\n"
}
], - "pdbx_nmr_spectrometer": [
- {
- "details": "string",
- "field_strength": 0.1,
- "manufacturer": "Varian, Bruker, JEOL, GE\n",
- "model": "AVANCE, AVANCE II, AVANCE III, AVANCE III HD, WH, WM, AC+, Alpha, AM, AMX, AMX II, DMX, DRX, DSX, MSL, OMEGA, OMEGA PSG, GX, GSX, A, AL, EC, EX, LA, ECP, Infinityplus, Mercury, VNMRS, VXR, UNITY, UNITY INOVA, UNITYPLUS, INOVA, home-built\n",
- "spectrometer_id": "1, 2, 3\n",
- "type": "Bruker WH, Bruker WM, Bruker AM, Bruker AMX, Bruker DMX, Bruker DRX, Bruker MSL, Bruker AVANCE, GE Omega, GE Omega PSG, JEOL GX, JEOL GSX, JEOL A, JEOL AL, JEOL EC, JEOL EX, JEOL LA, JEOL ECP, Varian VXRS, Varian UNITY, Varian UNITYplus, Varian INOVA, other\n"
}
], - "pdbx_reflns_twin": [
- {
- "crystal_id": "string",
- "diffrn_id": "string",
- "domain_id": "string",
- "fraction": 0.1,
- "operator": "h,-h-k,-l, h+k,-k,-l, -h,-k,l, h,-k,-l, h,-h-k,-l, -h,-k,l, k,-h,l\n",
- "type": "epitaxial"
}
], - "pdbx_related_exp_data_set": [
- {
- "data_reference": "10.000/10002/image_data/cif\n",
- "data_set_type": "diffraction image data, NMR free induction decay data\n",
- "details": "string",
- "metadata_reference": "10.000/10002/image_data/txt\n"
}
], - "pdbx_serial_crystallography_data_reduction": [
- {
- "crystal_hits": 0,
- "diffrn_id": "1",
- "droplet_hits": 0,
- "frame_hits": 0,
- "frames_failed_index": 0,
- "frames_indexed": 0,
- "frames_total": 0,
- "lattices_indexed": 0,
- "lattices_merged": 0,
- "xfel_pulse_events": 0,
- "xfel_run_numbers": "string"
}
], - "pdbx_serial_crystallography_measurement": [
- {
- "collection_time_total": 0.1,
- "collimation": "Kirkpatrick-Baez mirrors, Beryllium compound refractive lenses, Fresnel zone plates\n",
- "diffrn_id": "1",
- "focal_spot_size": 0.1,
- "photons_per_pulse": 0.1,
- "pulse_duration": 0.1,
- "pulse_energy": 0.1,
- "pulse_photon_energy": 0.1,
- "source_distance": 0.1,
- "source_size": 0.1,
- "xfel_pulse_repetition_rate": 0.1
}
], - "pdbx_serial_crystallography_sample_delivery": [
- {
- "description": "fixed target, electrospin, MESH, CoMESH, gas dynamic virtual nozzle, LCP injector, addressable microarray\n",
- "diffrn_id": "1",
- "method": "fixed target"
}
], - "pdbx_serial_crystallography_sample_delivery_fixed_target": [
- {
- "crystals_per_unit": 0,
- "description": "string",
- "details": "string",
- "diffrn_id": "1",
- "motion_control": "DMC-4080\n",
- "sample_dehydration_prevention": "seal, humidifed gas, flash freezing\n",
- "sample_holding": "mesh, loop, grid\n",
- "sample_solvent": "string",
- "sample_unit_size": 0.1,
- "support_base": "goniometer\n",
- "velocity_horizontal": 0.1,
- "velocity_vertical": 0.1
}
], - "pdbx_serial_crystallography_sample_delivery_injection": [
- {
- "carrier_solvent": "LCP, grease, liquid\n",
- "crystal_concentration": 0.1,
- "description": "microextrusion injector\n",
- "diffrn_id": "1",
- "filter_size": 0.1,
- "flow_rate": 0.1,
- "injector_diameter": 0.1,
- "injector_nozzle": "gas, GDVN\n",
- "injector_pressure": 0.1,
- "injector_temperature": 0.1,
- "jet_diameter": 0.1,
- "power_by": "syringe, gas, electronic potential\n",
- "preparation": "Crystals transfered to carrier solvent at room temperature\n"
}
], - "pdbx_soln_scatter": [
- {
- "buffer_name": "acetic acid\n",
- "concentration_range": "0.7 - 14\n",
- "data_analysis_software_list": "SCTPL5 GNOM\n",
- "data_reduction_software_list": "OTOKO\n",
- "detector_specific": "string",
- "detector_type": "string",
- "id": "string",
- "max_mean_cross_sectional_radii_gyration": 0.1,
- "max_mean_cross_sectional_radii_gyration_esd": 0.1,
- "mean_guiner_radius": 0.1,
- "mean_guiner_radius_esd": 0.1,
- "min_mean_cross_sectional_radii_gyration": 0.1,
- "min_mean_cross_sectional_radii_gyration_esd": 0.1,
- "num_time_frames": 0,
- "protein_length": "string",
- "sample_pH": 0.1,
- "source_beamline": "string",
- "source_beamline_instrument": "string",
- "source_class": "neutron source, synchrotron\n",
- "source_type": "string",
- "temperature": 0.1,
- "type": "modelling"
}
], - "pdbx_soln_scatter_model": [
- {
- "conformer_selection_criteria": "The modelled scattering curves were assessed by calculation of the\n RG, RSX-1 and RXS-2 values in the same Q ranges\n used in the experimental Guinier fits. models were\n then ranked using a goodness-of-fit R-factor\n defined by analogy with protein crystallography\n and based on the experimental curves in the Q range\n extending to 1.4 nm-1.\n",
- "details": "Homology models were built for\n the 17 SCR domains and energy minimisations were\n performed to improve the connectivity in the fh model.\n triantennary complex-type carbohydrate structures\n (MAN3GLCNAC6GAL3FUC3NEUNAC1) were added to each of the\n N-linked glycosylation sites. a library of linker peptide\n conformations was used in domain modelling constrained\n by the solution scattering fits. modelling with the\n scattering data was also carried out by rotational\n search methods. the x-ray and neutron scattering curve\n I(Q) was calculated assuming a uniform scattering density\n for the spheres using the debye equation as adapted to\n spheres. x-ray curves were calculated from the hydrated\n sphere models without corrections for wavelength spread or\n beam divergence, while these corrections were applied for\n the neutron curves but now using unhydrated models.\n",
- "entry_fitting_list": "PDB CODE 1HFI, 1HCC, 1HFH, 1VCC\n",
- "id": "string",
- "method": "Constrained scattering fitting of homology models\n",
- "num_conformers_calculated": 0,
- "num_conformers_submitted": 0,
- "representative_conformer": 0,
- "scatter_id": "string",
- "software_author_list": "MSI\n",
- "software_list": "INSIGHT II, HOMOLOGY, DISCOVERY, BIOPOLYMER, DELPHI\n"
}
], - "pdbx_vrpt_summary": {
- "RNA_suiteness": 0.1,
- "attempted_validation_steps": "string",
- "ligands_for_buster_report": "N",
- "report_creation_date": "2019-08-24T14:15:22Z",
- "restypes_notchecked_for_bond_angle_geometry": [
- "string"
]
}, - "pdbx_vrpt_summary_diffraction": [
- {
- "B_factor_type": "FULL",
- "Babinet_b": 0.1,
- "Babinet_k": 0.1,
- "CCP4_version": "string",
- "DCC_R": 0.1,
- "DCC_Rfree": 0.1,
- "EDS_R": 0.1,
- "EDS_R_warning": "string",
- "EDS_res_high": 0.1,
- "EDS_res_low": 0.1,
- "Fo_Fc_correlation": 0.1,
- "I_over_sigma": "string",
- "Padilla_Yeates_L2_mean": 0.1,
- "Padilla_Yeates_L_mean": 0.1,
- "Q_score": 0.1,
- "Wilson_B_aniso": "string",
- "Wilson_B_estimate": 0.1,
- "acentric_outliers": 0,
- "bulk_solvent_b": 0.1,
- "bulk_solvent_k": 0.1,
- "centric_outliers": 0,
- "data_anisotropy": 0.1,
- "data_completeness": 0.1,
- "density_fitness_version": "string",
- "exp_method": "string",
- "num_miller_indices": 0,
- "number_reflns_R_free": 0,
- "percent_RSRZ_outliers": 0.1,
- "percent_free_reflections": 0.1,
- "servalcat_version": "string",
- "trans_NCS_details": "The largest off-origin peak in the Patterson function is 8.82% of the height of the origin peak. No significant pseudotranslation is detected.\n",
- "twin_fraction": "h,h-k,h-l:0.477;-h,-h+k,-l:0.020;-h,-k,-h+l:0.017\n"
}
], - "pdbx_vrpt_summary_em": [
- {
- "Q_score": 0.1,
- "atom_inclusion_all_atoms": 0.1,
- "atom_inclusion_backbone": 0.1,
- "author_provided_fsc_resolution_by_cutoff_halfbit": 0.1,
- "author_provided_fsc_resolution_by_cutoff_onebit": 0.1,
- "author_provided_fsc_resolution_by_cutoff_pt_143": 0.1,
- "author_provided_fsc_resolution_by_cutoff_pt_333": 0.1,
- "author_provided_fsc_resolution_by_cutoff_pt_5": 0.1,
- "author_provided_fsc_resolution_by_cutoff_threesigma": 0.1,
- "calculated_fsc_resolution_by_cutoff_halfbit": 0.1,
- "calculated_fsc_resolution_by_cutoff_onebit": 0.1,
- "calculated_fsc_resolution_by_cutoff_pt_143": 0.1,
- "calculated_fsc_resolution_by_cutoff_pt_333": 0.1,
- "calculated_fsc_resolution_by_cutoff_pt_5": 0.1,
- "calculated_fsc_resolution_by_cutoff_threesigma": 0.1,
- "contour_level_primary_map": 0.1,
- "exp_method": "string"
}
], - "pdbx_vrpt_summary_geometry": [
- {
- "angles_RMSZ": 0.1,
- "bonds_RMSZ": 0.1,
- "clashscore": 0.1,
- "clashscore_full_length": 0.1,
- "num_H_reduce": 0,
- "num_angles_RMSZ": 0,
- "num_bonds_RMSZ": 0,
- "percent_ramachandran_outliers": 0.1,
- "percent_ramachandran_outliers_full_length": 0.1,
- "percent_rotamer_outliers": 0.1,
- "percent_rotamer_outliers_full_length": 0.1
}
], - "pdbx_vrpt_summary_nmr": [
- {
- "chemical_shift_completeness": 0.1,
- "chemical_shift_completeness_full_length": 0.1,
- "cyrange_error": "string",
- "cyrange_number_of_domains": 0,
- "exp_method": "string",
- "medoid_model": 0,
- "nmr_models_consistency_flag": "string",
- "nmrclust_error": "string",
- "nmrclust_number_of_clusters": 0,
- "nmrclust_number_of_models": 0,
- "nmrclust_number_of_outliers": 0,
- "nmrclust_representative_model": 0
}
], - "rcsb_accession_info": {
- "deposit_date": "2019-08-24T14:15:22Z",
- "has_released_experimental_data": "Y, N\n",
- "initial_release_date": "2019-08-24T14:15:22Z",
- "major_revision": 0,
- "minor_revision": 0,
- "revision_date": "2019-08-24T14:15:22Z",
- "status_code": "REL\n"
}, - "rcsb_comp_model_provenance": {
- "entry_id": "AF-P60325-F1, ma-bak-cepc-0019\n",
- "source_db": "AlphaFoldDB",
- "source_filename": "string",
- "source_pae_url": "string",
- "source_url": "string"
}, - "rcsb_entry_container_identifiers": {
- "assembly_ids": [
- "string"
], - "branched_entity_ids": [
- "string"
], - "emdb_ids": [
- "string"
], - "entity_ids": [
- "string"
], - "entry_id": "4HHB, AF_AFP60325F1, MA_MABAKCEPC0019\n",
- "model_ids": [
- 0
], - "non_polymer_entity_ids": [
- "string"
], - "polymer_entity_ids": [
- "string"
], - "rcsb_id": "1KIP\n",
- "related_emdb_ids": [
- "string"
], - "water_entity_ids": [
- "string"
], - "pubmed_id": 0
}, - "rcsb_entry_info": {
- "assembly_count": 0,
- "branched_entity_count": 0,
- "branched_molecular_weight_maximum": 0.1,
- "branched_molecular_weight_minimum": 0.1,
- "cis_peptide_count": 0,
- "deposited_atom_count": 0,
- "deposited_deuterated_water_count": 0,
- "deposited_hydrogen_atom_count": 0,
- "deposited_model_count": 0,
- "deposited_modeled_polymer_monomer_count": 0,
- "deposited_nonpolymer_entity_instance_count": 0,
- "deposited_polymer_entity_instance_count": 0,
- "deposited_polymer_monomer_count": 0,
- "deposited_solvent_atom_count": 0,
- "deposited_unmodeled_polymer_monomer_count": 0,
- "diffrn_radiation_wavelength_maximum": 0.1,
- "diffrn_radiation_wavelength_minimum": 0.1,
- "disulfide_bond_count": 0,
- "entity_count": 0,
- "experimental_method": "X-ray\n",
- "experimental_method_count": 0,
- "inter_mol_covalent_bond_count": 0,
- "inter_mol_metalic_bond_count": 0,
- "molecular_weight": 0.1,
- "na_polymer_entity_types": "DNA (only)\n",
- "ndb_struct_conf_na_feature_combined": "a-form double helix",
- "nonpolymer_bound_components": [
- "string"
], - "nonpolymer_entity_count": 0,
- "nonpolymer_molecular_weight_maximum": 0.1,
- "nonpolymer_molecular_weight_minimum": 0.1,
- "polymer_composition": "homomeric protein\n",
- "polymer_entity_count": 0,
- "polymer_entity_count_DNA": 0,
- "polymer_entity_count_RNA": 0,
- "polymer_entity_count_nucleic_acid": 0,
- "polymer_entity_count_nucleic_acid_hybrid": 0,
- "polymer_entity_count_protein": 0,
- "polymer_entity_taxonomy_count": 0,
- "polymer_molecular_weight_maximum": 0.1,
- "polymer_molecular_weight_minimum": 0.1,
- "polymer_monomer_count_maximum": 0,
- "polymer_monomer_count_minimum": 0,
- "resolution_combined": [
- 0.1
], - "selected_polymer_entity_types": "Protein (only)\n",
- "software_programs_combined": [
- "string"
], - "solvent_entity_count": 0,
- "structure_determination_methodology": "experimental\n",
- "structure_determination_methodology_priority": 0,
- "diffrn_resolution_high": {
- "provenance_source": "Depositor assigned",
- "value": 0.1
}
}, - "rcsb_ma_qa_metric_global": [
- {
- "model_id": 0,
- "ma_qa_metric_global": [
- {
- "description": "confidence score predicting accuracy according to the CA-only Local Distance Difference Test (lDDT-CA) in [0,100]\n",
- "name": "pLDDT\n",
- "type": "pLDDT\n",
- "type_other_details": "string",
- "value": 0.1
}
]
}
], - "rcsb_primary_citation": {
- "book_id_ISBN": "string",
- "book_publisher": "John Wiley and Sons\n",
- "book_publisher_city": "London\n",
- "book_title": "string",
- "coordinate_linkage": "n",
- "country": "string",
- "id": "primary\n",
- "journal_abbrev": "J.Mol.Biol., J. Mol. Biol.\n",
- "journal_id_ASTM": "string",
- "journal_id_CSD": "0070\n",
- "journal_id_ISSN": "string",
- "journal_issue": "2",
- "journal_volume": "174",
- "language": "German\n",
- "page_first": "string",
- "page_last": "string",
- "pdbx_database_id_DOI": "10.2345/S1384107697000225\n",
- "pdbx_database_id_PubMed": 0,
- "rcsb_ORCID_identifiers": [
- "string"
], - "rcsb_authors": [
- "string"
], - "rcsb_journal_abbrev": "Nat Struct Mol Biol\n",
- "title": "Structure of diferric duck ovotransferrin\n at 2.35 Angstroms resolution.\n",
- "year": 0
}, - "refine": [
- {
- "B_iso_max": 0.1,
- "B_iso_mean": 0.1,
- "B_iso_min": 0.1,
- "aniso_B_1_1": 0.1,
- "aniso_B_1_2": 0.1,
- "aniso_B_1_3": 0.1,
- "aniso_B_2_2": 0.1,
- "aniso_B_2_3": 0.1,
- "aniso_B_3_3": 0.1,
- "correlation_coeff_Fo_to_Fc": 0.1,
- "correlation_coeff_Fo_to_Fc_free": 0.1,
- "details": "HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS\n",
- "ls_R_factor_R_free": 0.1,
- "ls_R_factor_R_free_error": 0.1,
- "ls_R_factor_R_free_error_details": "string",
- "ls_R_factor_R_work": 0.1,
- "ls_R_factor_all": 0.1,
- "ls_R_factor_obs": 0.1,
- "ls_d_res_high": 0.1,
- "ls_d_res_low": 0.1,
- "ls_matrix_type": "atomblock",
- "ls_number_parameters": 0,
- "ls_number_reflns_R_free": 0,
- "ls_number_reflns_R_work": 0,
- "ls_number_reflns_all": 0,
- "ls_number_reflns_obs": 0,
- "ls_number_restraints": 0,
- "ls_percent_reflns_R_free": 0.1,
- "ls_percent_reflns_obs": 0.1,
- "ls_redundancy_reflns_all": 0.1,
- "ls_redundancy_reflns_obs": 0.1,
- "ls_wR_factor_R_free": 0.1,
- "ls_wR_factor_R_work": 0.1,
- "occupancy_max": 0.1,
- "occupancy_min": 0.1,
- "overall_FOM_free_R_set": 0.1,
- "overall_FOM_work_R_set": 0.1,
- "overall_SU_B": 0.1,
- "overall_SU_ML": 0.1,
- "overall_SU_R_Cruickshank_DPI": 0.1,
- "overall_SU_R_free": 0.1,
- "pdbx_R_Free_selection_details": "Random selection\n",
- "pdbx_TLS_residual_ADP_flag": "LIKELY RESIDUAL",
- "pdbx_average_fsc_free": 0.1,
- "pdbx_average_fsc_overall": 0.1,
- "pdbx_average_fsc_work": 0.1,
- "pdbx_data_cutoff_high_absF": 0.1,
- "pdbx_data_cutoff_high_rms_absF": 0.1,
- "pdbx_data_cutoff_low_absF": 0.1,
- "pdbx_diffrn_id": [
- "string"
], - "pdbx_isotropic_thermal_model": "Isotropic, Overall\n",
- "pdbx_ls_cross_valid_method": "FREE R-VALUE\n",
- "pdbx_ls_sigma_F": 0.1,
- "pdbx_ls_sigma_Fsqd": 0.1,
- "pdbx_ls_sigma_I": 0.1,
- "pdbx_method_to_determine_struct": "AB INITIO PHASING, DM, ISAS, ISIR, ISIRAS, MAD, MIR, MIRAS, MR, SIR, SIRAS\n",
- "pdbx_overall_ESU_R": 0.1,
- "pdbx_overall_ESU_R_Free": 0.1,
- "pdbx_overall_SU_R_Blow_DPI": 0.1,
- "pdbx_overall_SU_R_free_Blow_DPI": 0.1,
- "pdbx_overall_SU_R_free_Cruickshank_DPI": 0.1,
- "pdbx_overall_phase_error": 0.1,
- "pdbx_refine_id": "string",
- "pdbx_solvent_ion_probe_radii": 0.1,
- "pdbx_solvent_shrinkage_radii": 0.1,
- "pdbx_solvent_vdw_probe_radii": 0.1,
- "pdbx_starting_model": "1XYZ, 2XYZ, BDL001\n",
- "pdbx_stereochem_target_val_spec_case": "string",
- "pdbx_stereochemistry_target_values": "string",
- "solvent_model_details": "string",
- "solvent_model_param_bsol": 0.1,
- "solvent_model_param_ksol": 0.1
}
], - "refine_analyze": [
- {
- "Luzzati_coordinate_error_free": 0.1,
- "Luzzati_coordinate_error_obs": 0.1,
- "Luzzati_d_res_low_free": 0.1,
- "Luzzati_d_res_low_obs": 0.1,
- "Luzzati_sigma_a_free": 0.1,
- "Luzzati_sigma_a_obs": 0.1,
- "number_disordered_residues": 0.1,
- "occupancy_sum_hydrogen": 0.1,
- "occupancy_sum_non_hydrogen": 0.1,
- "pdbx_Luzzati_d_res_high_obs": 0.1,
- "pdbx_refine_id": "string"
}
], - "refine_hist": [
- {
- "cycle_id": "string",
- "d_res_high": 0.1,
- "d_res_low": 0.1,
- "number_atoms_solvent": 0,
- "number_atoms_total": 0,
- "pdbx_B_iso_mean_ligand": 0.1,
- "pdbx_B_iso_mean_solvent": 0.1,
- "pdbx_number_atoms_ligand": 0,
- "pdbx_number_atoms_nucleic_acid": 0,
- "pdbx_number_atoms_protein": 0,
- "pdbx_number_residues_total": 0,
- "pdbx_refine_id": "string"
}
], - "refine_ls_restr": [
- {
- "dev_ideal": 0.1,
- "dev_ideal_target": 0.1,
- "number": 0,
- "pdbx_refine_id": "string",
- "pdbx_restraint_function": "SINUSOIDAL, HARMONIC, SEMIHARMONIC\n",
- "type": "p_bond_d, p_angle_d, p_planar_d, p_xhbond_d, p_xhangle_d, p_hydrog_d, p_special_d, p_planar, p_chiral, p_singtor_nbd, p_multtor_nbd, p_xyhbond_nbd, p_xhyhbond_nbd, p_special_tor, p_planar_tor, p_staggered_tor, p_orthonormal_tor, p_mcbond_it, p_mcangle_it, p_scbond_it, p_scangle_it, p_xhbond_it, p_xhangle_it, p_special_it, RESTRAIN_Distances < 2.12, RESTRAIN_Distances 2.12 < D < 2.625, RESTRAIN_Distances > 2.625, RESTRAIN_Peptide Planes, RESTRAIN_Ring and other planes, RESTRAIN_rms diffs for Uiso atoms at dist 1.2-1.4, RESTRAIN_rms diffs for Uiso atoms at dist 1.4-1.6, RESTRAIN_rms diffs for Uiso atoms at dist 1.8-2.0, RESTRAIN_rms diffs for Uiso atoms at dist 2.0-2.2, RESTRAIN_rms diffs for Uiso atoms at dist 2.2-2.4, RESTRAIN_rms diffs for Uiso atoms at dist >2.4\n",
- "weight": 0.1
}
], - "reflns": [
- {
- "B_iso_Wilson_estimate": 0.1,
- "R_free_details": "The data set was sorted with l varying most\n rapidly and h varying least rapidly. Every\n 10th reflection in this sorted list was\n excluded from refinement and included in the\n calculation of a 'free' R factor.\n",
- "Rmerge_F_all": 0.1,
- "Rmerge_F_obs": 0.1,
- "d_resolution_high": 0.1,
- "d_resolution_low": 0.1,
- "data_reduction_details": "Merging and scaling based on only those\n reflections with I > sig(I).\n",
- "data_reduction_method": "Profile fitting by method of Kabsch (1987).\n Scaling used spherical harmonic coefficients.\n",
- "details": "string",
- "limit_h_max": 0,
- "limit_h_min": 0,
- "limit_k_max": 0,
- "limit_k_min": 0,
- "limit_l_max": 0,
- "limit_l_min": 0,
- "number_all": 0,
- "number_obs": 0,
- "observed_criterion": ">2sigma(I)\n",
- "observed_criterion_F_max": 0.1,
- "observed_criterion_F_min": 0.1,
- "observed_criterion_I_max": 0.1,
- "observed_criterion_I_min": 0.1,
- "observed_criterion_sigma_F": 0.1,
- "observed_criterion_sigma_I": 0.1,
- "pdbx_CC_half": 0.1,
- "pdbx_R_split": 0.1,
- "pdbx_Rmerge_I_obs": 0.1,
- "pdbx_Rpim_I_all": 0.1,
- "pdbx_Rrim_I_all": 0.1,
- "pdbx_Rsym_value": 0.1,
- "pdbx_chi_squared": 0.1,
- "pdbx_diffrn_id": [
- "string"
], - "pdbx_netI_over_av_sigmaI": 0.1,
- "pdbx_netI_over_sigmaI": 0.1,
- "pdbx_number_measured_all": 0,
- "pdbx_ordinal": 0,
- "pdbx_redundancy": 0.1,
- "pdbx_scaling_rejects": 0,
- "percent_possible_obs": 0.1,
- "phase_calculation_details": "From model, NCS averaging, Solvent flipping, Solvent flattening, Multiple crystal averaging, Multiple phase modification, Other phase modification\n"
}
], - "reflns_shell": [
- {
- "Rmerge_F_all": 0.1,
- "Rmerge_F_obs": 0.1,
- "Rmerge_I_all": 0.1,
- "Rmerge_I_obs": 0.1,
- "d_res_high": 0.1,
- "d_res_low": 0.1,
- "meanI_over_sigI_all": 0.1,
- "meanI_over_sigI_obs": 0.1,
- "meanI_over_uI_all": 0.1,
- "number_measured_all": 0,
- "number_measured_obs": 0,
- "number_possible": 0,
- "number_unique_all": 0,
- "number_unique_obs": 0,
- "pdbx_CC_half": 0.1,
- "pdbx_R_split": 0.1,
- "pdbx_Rpim_I_all": 0.1,
- "pdbx_Rrim_I_all": 0.1,
- "pdbx_Rsym_value": 0.1,
- "pdbx_chi_squared": 0.1,
- "pdbx_diffrn_id": [
- "string"
], - "pdbx_netI_over_sigmaI_all": 0.1,
- "pdbx_netI_over_sigmaI_obs": 0.1,
- "pdbx_ordinal": 0,
- "pdbx_redundancy": 0.1,
- "pdbx_rejects": 0,
- "percent_possible_all": 0.1,
- "percent_possible_obs": 0.1
}
], - "software": [
- {
- "citation_id": "string",
- "classification": "data collection, data reduction, phasing, model building, refinement, validation, other\n",
- "contact_author": "T. Alwyn Jones, Axel Brunger\n",
- "contact_author_email": "bourne@sdsc.edu\n",
- "date": "1991-10-01, 1990-04-30\n",
- "description": "Uses method of restrained least squares\n",
- "language": "Ada",
- "location": "http://rosebud.sdsc.edu/projects/pb/IUCr/software.html, ftp://ftp.sdsc.edu/pub/sdsc/biology/\n",
- "name": "Merlot, O, Xengen, X-plor\n",
- "os": "Ultrix, OpenVMS, DOS, Windows 95, Windows NT, Irix, HPUX, DEC Unix\n",
- "pdbx_ordinal": 0,
- "type": "filter",
- "version": "v1.0, beta, 3.1-2, unknown\n"
}
], - "struct": {
- "pdbx_CASP_flag": "Y\n",
- "pdbx_descriptor": "Cytochrome b5, Regulatory protein RecX, Uridine kinase (E.C.2.7.1.48)\n",
- "pdbx_model_details": "This model was produced from a 10 nanosecond Amber/MD simulation\nstarting from PDB structure ID 1ABC.\n",
- "pdbx_model_type_details": "MINIMIZED AVERAGE\n",
- "title": "T4 lysozyme mutant - S32A, Rhinovirus 16 polymerase elongation complex (r1_form), Crystal structure of the OXA-10 W154A mutant at pH 9.0, Mutant structure of Thermus thermophilus HB8 uridine-cytidine kinase, Crystal structure of xylanase from Trichoderma longibrachiatum\n"
}, - "struct_keywords": {
- "pdbx_keywords": "DNA, RNA, T-RNA, DNA/RNA, RIBOZYME, PROTEIN/DNA, PROTEIN/RNA, PEPTIDE NUCLEIC ACID, PEPTIDE NUCLEIC ACID/DNA, DNA-BINDING PROTEIN, RNA-BINDING PROTEIN\n",
- "text": "Inhibitor, Complex, Isomerase..., serine protease, inhibited complex, high-resolution refinement\n"
}, - "symmetry": {
- "Int_Tables_number": 0,
- "cell_setting": "cubic",
- "pdbx_full_space_group_name_H_M": "Example: 'C 1 2 1' (instead of C 2)\n 'P 1 2 1' (instead of P 2)\n 'P 1 21 1' (instead of P 21)\n 'P 1 1 21' (instead of P 21 -unique C axis)\n 'H 3' (instead of R 3 -hexagonal)\n 'H 3 2' (instead of R 3 2 -hexagonal)\n",
- "space_group_name_H_M": "A 1, A 1 2 1, A 2, B 1 1 2, B 2, B 2 21 2, C 2, C 1 2 1, C 21, C 1 21 1, C 2(A 112), C 2 2 2, C 2 2 21, C 4 21 2, F 2 2 2, F 2 3, F 4 2 2, F 4 3 2, F 41 3 2, I 1 2 1, I 1 21 1, I 2, I 2 2 2, I 2 3, I 21, I 21 3, I 21 21 21, I 4, I 4 2 2, I 4 3 2, I 41, I 41/a, I 41 2 2, I 41 3 2, P 1, P 1-, P 2, P 1 2 1, P 1 1 2, P 2 2 2, P 2 3, P 2 2 21, P 2 21 21, P 21, P 1 21 1, P 1 21/c 1, P 1 1 21, P 21(C), P 21 2 21, P 21 3, P 21 21 2, P 21 21 2 A, P 21 21 21, P 3, P 3 1 2, P 3 2 1, P 31, P 31 1 2, P 31 2 1, P 32, P 32 1 2, P 32 2 1, P 4, P 4 2 2, P 4 3 2, P 4 21 2, P 41, P 41 2 2, P 41 3 2, P 41 21 2, P 42, P 42 2 2, P 42 3 2, P 42 21 2, P 43, P 43 2 2, P 43 3 2, P 43 21 2, P 6, P 6 2 2, P 61, P 61 2 2, P 62, P 62 2 2, P 63, P 63 2 2, P 64, P 64 2 2, P 65, P 65 2 2, H 3, R 3, H 3 2, R 3 2\n",
- "space_group_name_Hall": "-P 2ac 2n, -R 3 2\", P 61 2 2 (0 0 -1)\n"
}, - "rcsb_id": "1KIP\n",
- "rcsb_entry_group_membership": [
- {
- "group_id": "G_1001001\n",
- "aggregation_method": "matching_deposit_group_id"
}
], - "rcsb_external_references": [
- {
- "id": "string",
- "type": "OLDERADO",
- "link": "string"
}
], - "rcsb_binding_affinity": [
- {
- "comp_id": "0WE, SPE, CL\n",
- "type": "IC50, EC50, Kd, Ka, Ki\n",
- "value": 0.1,
- "unit": "nM, kJ/mol\n",
- "symbol": "~, =, >, <, >=, <=\n",
- "reference_sequence_identity": 0,
- "provenance_code": "PDBBind",
- "link": "string"
}
]
}
entry_id required | string Example: 4ACQ ENTRY ID of the entry. |
{- "rcsb_id": "string",
- "rcsb_pubmed_container_identifiers": {
- "pubmed_id": 0
}, - "rcsb_pubmed_central_id": "string",
- "rcsb_pubmed_doi": "string",
- "rcsb_pubmed_abstract_text": "string",
- "rcsb_pubmed_affiliation_info": [
- "string"
], - "rcsb_pubmed_mesh_descriptors": [
- "string"
], - "rcsb_pubmed_mesh_descriptors_lineage": [
- {
- "id": "E01.370.225.500.388, H01.181\n",
- "name": "Chemistry, Mammals, Therapeutic Uses\n",
- "depth": 0
}
]
}
provides access to groups formed by aggregating individual structures, sequences or assemblies that share a degree of similarity
group_id required | string Example: Q3Y9I6 Group ID |
{- "rcsb_id": "string",
- "rcsb_group_container_identifiers": {
- "group_id": "string",
- "group_provenance_id": "provenance_sequence_identity",
- "parent_member_ids": [
- "string"
], - "group_member_ids": [
- "string"
]
}, - "rcsb_group_info": {
- "group_name": "string",
- "group_description": "string",
- "group_members_granularity": "assembly",
- "group_members_count": 0
}, - "rcsb_group_statistics": {
- "similarity_cutoff": 0.1,
- "similarity_score_min": 0.1,
- "similarity_score_max": 0.1
}, - "rcsb_group_accession_info": {
- "version": 0
}, - "rcsb_group_related": [
- {
- "resource_accession_code": "P69905\n",
- "resource_name": "UniProt\n"
}
]
}
group_provenance_id required | string Example: provenance_sequence_identity Group provenance ID |
{- "rcsb_id": "string",
- "rcsb_group_provenance_container_identifiers": {
- "group_provenance_id": "provenance_sequence_identity"
}, - "rcsb_group_aggregation_method": {
- "type": "sequence_identity",
- "method": {
- "name": "mmseqs2\n",
- "version": "v1.0, 3.1-2, unknown\n",
- "details": [
- {
- "type": "string",
- "name": "string",
- "value": 0.1,
- "description": "string"
}
]
}, - "similarity_criteria": {
- "similarity_function": "RMSD\n"
}
}
}
group_id required | string Example: Q3Y9I6 Group ID |
{- "rcsb_id": "string",
- "rcsb_group_container_identifiers": {
- "group_id": "string",
- "group_provenance_id": "provenance_sequence_identity",
- "parent_member_ids": [
- "string"
], - "group_member_ids": [
- "string"
]
}, - "rcsb_group_info": {
- "group_name": "string",
- "group_description": "string",
- "group_members_granularity": "assembly",
- "group_members_count": 0
}, - "rcsb_group_statistics": {
- "similarity_cutoff": 0.1,
- "similarity_score_min": 0.1,
- "similarity_score_max": 0.1
}, - "rcsb_group_accession_info": {
- "version": 0
}, - "rcsb_group_related": [
- {
- "resource_accession_code": "P69905\n",
- "resource_name": "UniProt\n"
}
], - "rcsb_polymer_entity_group_members_rankings": [
- {
- "ranking_criteria_type": "coverage",
- "group_members": [
- {
- "member_id": "string",
- "rank": 0,
- "original_score": 0.1
}
]
}
], - "rcsb_polymer_entity_group_sequence_alignment": {
- "abstract_reference": {
- "length": 0,
- "sequence": "string"
}, - "group_members_alignment": [
- {
- "member_id": "string",
- "scores": {
- "target_coverage": 0,
- "query_coverage": 0,
- "target_length": 0,
- "query_length": 0
}, - "aligned_regions": [
- [
- 0
]
]
}
]
}
}
provides access to information about pairwise polymeric interfaces present in assemblies
entry_id required | string Example: 1RH7 ENTRY ID of the entry. |
assembly_id required | string Example: 1 ASSEMBLY ID of the biological assembly. |
interface_id required | string Example: 1 INTERFACE ID of the pairwise polymeric interface. |
{- "rcsb_id": "string",
- "rcsb_interface_container_identifiers": {
- "entry_id": "string",
- "assembly_id": "string",
- "interface_id": "1, 2\n",
- "interface_entity_id": "1, 2\n",
- "rcsb_id": "2UZI-1.A.B?1\n"
}, - "rcsb_interface_partner": [
- {
- "interface_partner_identifier": {
- "entity_id": "string",
- "asym_id": "string"
}, - "interface_partner_feature": [
- {
- "assignment_version": "V4_0_2\n",
- "description": "string",
- "feature_id": "string",
- "name": "string",
- "provenance_source": "NACCESS\n",
- "type": "ASA_UNBOUND, BINDING_SITE\n",
- "feature_positions": [
- {
- "beg_seq_id": 0,
- "end_seq_id": 0,
- "values": [
- 0.1
]
}
], - "additional_properties": [
- {
- "name": "TO_BE_DEFINED\n",
- "values": [
- { }
]
}
]
}
]
}, - {
- "interface_partner_identifier": {
- "entity_id": "string",
- "asym_id": "string"
}, - "interface_partner_feature": [
- {
- "assignment_version": "V4_0_2\n",
- "description": "string",
- "feature_id": "string",
- "name": "string",
- "provenance_source": "NACCESS\n",
- "type": "ASA_UNBOUND, BINDING_SITE\n",
- "feature_positions": [
- {
- "beg_seq_id": 0,
- "end_seq_id": 0,
- "values": [
- 0.1
]
}
], - "additional_properties": [
- {
- "name": "TO_BE_DEFINED\n",
- "values": [
- { }
]
}
]
}
]
}
], - "rcsb_interface_operator": [
- [
- [
- "string"
]
]
], - "rcsb_interface_info": {
- "polymer_composition": "Nucleic acid (only)",
- "interface_character": "homo",
- "interface_area": 0.1,
- "self_jaccard_contact_score": 0.1,
- "num_interface_residues": 0,
- "num_core_interface_residues": 0
}, - "rcsb_latest_revision": {
- "major_revision": 0,
- "minor_revision": 0,
- "revision_date": "2019-08-24T14:15:22Z"
}
}
entry_id required | string ID of the entry that needs to be fetched. |
{- "rcsb_repository_holdings_combined": {
- "id_code_replaced_by_latest": "4HHB\n",
- "status": "CURRENT\n",
- "status_code": "HPUB\n"
}, - "rcsb_repository_holdings_combined_entry_container_identifiers": {
- "entry_id": "1KIP\n",
- "rcsb_id": "1KIP\n",
- "update_id": "2018_23\n"
}, - "rcsb_id": "1KIP\n"
}
ids required | string A comma separated entry ID list. |
[- {
- "rcsb_repository_holdings_combined": {
- "id_code_replaced_by_latest": "4HHB\n",
- "status": "CURRENT\n",
- "status_code": "HPUB\n"
}, - "rcsb_repository_holdings_combined_entry_container_identifiers": {
- "entry_id": "1KIP\n",
- "rcsb_id": "1KIP\n",
- "update_id": "2018_23\n"
}, - "rcsb_id": "1KIP\n"
}
]
entry_id required | string Example: 1HHB ID of the entry that needs to be fetched. |
{- "rcsb_repository_holdings_insilico_models": {
- "audit_authors": [
- "string"
], - "deposit_date": "2019-08-24T14:15:22Z",
- "id_codes_replaced_by": [
- "string"
], - "release_date": "2019-08-24T14:15:22Z",
- "remove_date": "2019-08-24T14:15:22Z",
- "status_code": "HPUB\n",
- "title": "The structure of this interesting pathogen molecule\n"
}, - "rcsb_repository_holdings_removed": {
- "audit_authors": [
- "string"
], - "deposit_date": "2019-08-24T14:15:22Z",
- "details": "An improved ligand starting model was found to significantly improve the model\nand refinement statistics for this entry.\n",
- "id_codes_replaced_by": [
- "string"
], - "release_date": "2019-08-24T14:15:22Z",
- "remove_date": "2019-08-24T14:15:22Z",
- "repository_content_types": "Combined NMR data (NEF)",
- "title": "The structure of this interesting pathogen molecule\n"
}, - "rcsb_repository_holdings_removed_audit_author": [
- {
- "audit_author": "Bleary, Percival R.\n",
- "ordinal_id": 0
}
], - "rcsb_repository_holdings_removed_entry_container_identifiers": {
- "entry_id": "1KIP\n",
- "rcsb_id": "1KIP\n",
- "update_id": "2019_24\n"
}, - "rcsb_repository_holdings_superseded": {
- "id_codes_superseded": [
- "string"
]
}, - "rcsb_repository_holdings_transferred": {
- "audit_authors": [
- "string"
], - "deposit_date": "2019-08-24T14:15:22Z",
- "release_date": "2019-08-24T14:15:22Z",
- "remote_accession_code": "ma-czyyf\n",
- "remote_repository_name": "Model Archive\n",
- "repository_content_types": "Combined NMR data (NEF)",
- "status_code": "HPUB\n",
- "title": "The structure of this interesting pathogen molecule\n"
}, - "rcsb_id": "1KIP\n"
}
ids required | string A comma separated unreleased entry ID list. |
[- {
- "rcsb_repository_holdings_prerelease": [
- {
- "entity_id": "1",
- "seq_one_letter_code": "HHHHAKQRSG..., AUCGGAAU..., (DG}(DA)(DT)(DA)(DT)...\n"
}
], - "rcsb_repository_holdings_unreleased": {
- "audit_authors": [
- "string"
], - "author_prerelease_sequence_status": "RELEASE IMMEDIATELY\n",
- "deposit_date": "2019-08-24T14:15:22Z",
- "deposit_date_coordinates": "2019-08-24T14:15:22Z",
- "deposit_date_nmr_restraints": "2019-08-24T14:15:22Z",
- "deposit_date_structure_factors": "2019-08-24T14:15:22Z",
- "hold_date_coordinates": "2019-08-24T14:15:22Z",
- "hold_date_nmr_restraints": "2019-08-24T14:15:22Z",
- "hold_date_structure_factors": "2019-08-24T14:15:22Z",
- "prerelease_sequence_available_flag": "Y\n",
- "release_date": "2019-08-24T14:15:22Z",
- "status_code": "HPUB\n",
- "title": "The structure of this interesting pathogen molecule\n"
}, - "rcsb_repository_holdings_unreleased_entry_container_identifiers": {
- "entry_id": "1KIP\n",
- "rcsb_id": "1KIP\n",
- "update_id": "2019_24\n"
}, - "rcsb_id": "1KIP\n"
}
]
entry_id required | string ID of the entry that needs to be fetched. |
{- "rcsb_repository_holdings_prerelease": [
- {
- "entity_id": "1",
- "seq_one_letter_code": "HHHHAKQRSG..., AUCGGAAU..., (DG}(DA)(DT)(DA)(DT)...\n"
}
], - "rcsb_repository_holdings_unreleased": {
- "audit_authors": [
- "string"
], - "author_prerelease_sequence_status": "RELEASE IMMEDIATELY\n",
- "deposit_date": "2019-08-24T14:15:22Z",
- "deposit_date_coordinates": "2019-08-24T14:15:22Z",
- "deposit_date_nmr_restraints": "2019-08-24T14:15:22Z",
- "deposit_date_structure_factors": "2019-08-24T14:15:22Z",
- "hold_date_coordinates": "2019-08-24T14:15:22Z",
- "hold_date_nmr_restraints": "2019-08-24T14:15:22Z",
- "hold_date_structure_factors": "2019-08-24T14:15:22Z",
- "prerelease_sequence_available_flag": "Y\n",
- "release_date": "2019-08-24T14:15:22Z",
- "status_code": "HPUB\n",
- "title": "The structure of this interesting pathogen molecule\n"
}, - "rcsb_repository_holdings_unreleased_entry_container_identifiers": {
- "entry_id": "1KIP\n",
- "rcsb_id": "1KIP\n",
- "update_id": "2019_24\n"
}, - "rcsb_id": "1KIP\n"
}
Provides access to the RCSB PDB data schemas. The data schema is powered by the JSON Schema (json-schema.org) language.