Legacy Fetch API Web Service
If your application currently uses Legacy Fetch API Web Service, it is important that you migrate to new GraphQL API and/or REST API so that your application continues to work.
Migration Guidelines Summary:
- New Data API specification is not backwards compatible with legacy APIs.
- New Data APIs return a JSON response. XML support is discontinued.
- All requests for data should be done through the new RCSB PDB Data API service.
Custom Reports
The /pdb/rest/customReport.xml service, that provided pre-defined summary and customizable
reports, is discontinued. Instead, use GraphQL API that allows writing flexible and declarative queries
to access PDB data. Refer to the
Data Attributes page for a full list of available attributes.
You can get an example GraphQL query for pre-defined reports available at rcsb.org:
- Select the report from Tabular Report dropdown
- Click on View GraphQL Query link
Descriptions
- Get descriptions for the whole PDB file
- Get descriptions for PDB entities
- Get descriptions of chemical components
- Get ligands that are present in a single PDB entry
PDB File Description Service
Describe PDB Entry
Access general information about a PDB entry (e.g., Header information).
Former endpoint: /pdb/rest/describePDB?structureId=4hhb
| Legacy API Field | GraphQL API Field |
|---|---|
| structureId | entry.entry.id |
| title | entry.struct.title |
| pubmedId | entry.rcsb_primary_citation.pdbx_database_id_PubMed |
| pubmedCentralId | entry.pubmed.rcsb_pubmed_central_id |
| expMethod | entry.rcsb_entry_info.experimental_method |
| resolution | entry.rcsb_entry_info.resolution_combined |
| replaces | entry.pdbx_database_PDB_obs_spr.replace_pdb_id |
| keywords | entry.struct_keywords.pdbx_keywords |
| nr_entities | entry.rcsb_entry_info.polymer_entity_count |
| nr_residues | entry.rcsb_entry_info.deposited_polymer_monomer_count |
| nr_atoms | entry.rcsb_entry_info.deposited_atom_count |
| deposition_date | entry.rcsb_accession_info.deposit_date |
| release_date | entry.rcsb_accession_info.initial_release_date |
| last_modification_date | entry.rcsb_accession_info.revision_date |
| structure_authors | entry.audit_author.name |
| citation_authors | entry.rcsb_primary_citation.rcsb_authors |
| status | N/A |
| relatedPDB.pdbId | entry.pdbx_database_related.db_id (content_type != 'split' & content_type != 're-refinement') |
| relatedPDB.details | entry.pdbx_database_related.details |
| originalStructureForRefinementPDB.pdbId | entry.pdbx_database_related.db_id (content_type == 're-refinement') |
| originalStructureForRefinementPDB.details | entry.pdbx_database_related.details |
| largeStructure | entry.pdbx_database_status.pdb_format_compatible = 'N' |
GraphQL Query:
Describe Molecular Entities
Describe the molecular entities that are contained in a PDB entry. Also provides information on the number
of available biological assemblies. Former endpoint /pdb/rest/getEntityInfo?structureId=1hv4.
| Legacy API Field | GraphQL API Field |
|---|---|
| structureId | entry.entry.id |
| bioAssemblies | entry.rcsb_entry_info.assembly_count |
| release_date | entry.rcsb_accession_info.initial_release_date |
| resolution | entry.rcsb_entry_info.resolution_combined |
| Method.name | entry.rcsb_entry_info.experimental_method |
| Entity.id | entry.polymer_entities.rcsb_polymer_entity_container_identifiers.entity_id |
| Entity.type | entry.polymer_entities.entity_poly.rcsb_entity_polymer_type |
| Chain.id | entry.polymer_entities.rcsb_polymer_entity_container_identifiers.auth_asym_ids |
GraphQL Query:
Descriptions of PDB entities
Access the descriptions of the entities that are contained in a PDB file.
Former endpoint /pdb/rest/describeMol?structureId=4hhb.
| Legacy API Field | GraphQL API Field |
|---|---|
| structureId | entry.entry.id |
| polymer.entityNr | entry.polymer_entities.rcsb_polymer_entity_container_identifiers.entry_id |
| chain.id | entry.polymer_entities.rcsb_polymer_entity_container_identifiers.auth_asym_ids |
| polymer.length | entry.polymer_entities.entity_poly.rcsb_sample_sequence_length |
| polymer.type | entry.polymer_entities.entity_poly.rcsb_entity_polymer_type |
| polymer.weight | entry.polymer_entities.rcsb_polymer_entity.formula_weight |
| Taxonomy.name | entry.polymer_entities.rcsb_entity_source_organism.ncbi_scientific_name |
| Taxonomy.id | entry.polymer_entities.rcsb_entity_source_organism.ncbi_taxonomy_id |
| synonym.name | entry.polymer_entities.rcsb_polymer_entity_name_com.name |
| macroMolecule.name | entry.polymer_entities.uniprots.rcsb_uniprot_protein.name.value |
| macroMolecule.accession.id | entry.polymer_entities.uniprots.rcsb_uniprot_container_identifiers.uniprot_id |
| polymerDescription.description | entry.polymer_entities.rcsb_polymer_entity.pdbx_description |
| fragment.desc | entry.polymer_entities.rcsb_polymer_entity.pdbx_fragment |
| enzClass.ec | entry.polymer_entities.rcsb_polymer_entity.pdbx_ec |
| mutation.desc | entry.polymer_entities.rcsb_polymer_entity.pdbx_mutation |
| details.desc | entry.polymer_entities.rcsb_polymer_entity.details |
GraphQL Query:
Descriptions of Chemical Components
Access the descriptions of the chemical components based on their IDs.
Former endpoint /pdb/rest/describeHet?chemicalID=NAG,EBW
| Legacy API Field | GraphQL API Field |
|---|---|
| chemicalID | chem_comps.chem_comp.id |
| type | chem_comps.chem_comp.type |
| molecularWeight | chem_comps.chem_comp.formula_weight |
| chemicalName | chem_comps.chem_comp.name |
| formula | chem_comps.chem_comp.formula |
| InChI | chem_comps.rcsb_chem_comp_descriptor.InChI |
| InChIKey | chem_comps.rcsb_chem_comp_descriptor.InChIKey |
| smiles | chem_comps.pdbx_chem_comp_descriptor.descriptor (pdbx_chem_comp_descriptor.type == 'SMILES_CANONICAL' & pdbx_chem_comp_descriptor.program == 'OpenEye OEToolkits') |
GraphQL Query:
Ligands in PDB Entry
List the ligands that can be found in a PDB entry. Former endpoint: /pdb/rest/ligandInfo?structureId=4HHB
| Legacy API Field | GraphQL API Field |
|---|---|
| structureId | entry.nonpolymer_entities.rcsb_nonpolymer_entity_container_identifiers.entry_id |
| chemicalID | entry.nonpolymer_entities.nonpolymer_comp.chem_comp.id |
| type | entry.nonpolymer_entities.nonpolymer_comp.chem_comp.type |
| molecularWeight | entry.nonpolymer_entities.nonpolymer_comp.chem_comp.formula_weight |
| chemicalName | entry.nonpolymer_entities.nonpolymer_comp.chem_comp.name |
| formula | entry.nonpolymer_entities.nonpolymer_comp.chem_comp.formula |
| InChI | entry.nonpolymer_entities.nonpolymer_comp.rcsb_chem_comp_descriptor.InChI |
| InChIKey | entry.nonpolymer_entities.nonpolymer_comp.rcsb_chem_comp_descriptor.InChIKey |
| smiles | entry.nonpolymer_entities.nonpolymer_comp.pdbx_chem_comp_descriptor.descriptor (pdbx_chem_comp_descriptor.type == 'SMILES_CANONICAL' & pdbx_chem_comp_descriptor.program == 'OpenEye OEToolkits') |
GraphQL Query:
Lists and Status
- Get a PDB ID's release status
- Get a list of all currently released PDB IDs
- Get a list of unreleased PDB IDs
- Get the pre-release sequences in FASTA format
- If there are biological assemblies, get the number of biological assemblies that are available for a PDB ID
Release Status
Get the status information of one PDB ID.
Former endpoint: /pdb/rest/idStatus?structureId=4HHB
Current endpoint:
https://data.rcsb.org/rest/v1/holdings/status/4HHB
Get the status information for a set of PDB IDs.
Former endpoint: /pdb/rest/idStatus?structureId=450D,451D
Current endpoint:
https://data.rcsb.org/rest/v1/holdings/status?ids=450D,451D
List Current/Obsolete PDB IDs
Get a list of all current PDB IDs.
Former endpoint: /pdb/json/getCurrent
Current endpoint:
https://data.rcsb.org/rest/v1/holdings/current/entry_ids
Get a list of all obsolete PDB IDs.
Former endpoint: /pdb/json/getObsolete
Current endpoint:
https://data.rcsb.org/rest/v1/holdings/removed/entry_ids
List Unreleased PDB IDs
Get a list of PDB IDs that have not been released yet.
Access the information for all unreleased PDB IDs.
Former endpoint: /pdb/rest/getUnreleased
Current endpoint: https://data.rcsb.org/rest/v1/holdings/unreleased/entry_ids
Access the information for a subset of PDB IDs.
Former endpoint: /pdb/rest/getUnreleased?structureId=450D,451D
Current endpoint: https://data.rcsb.org/rest/v1/holdings/unreleased?ids=450D,451D
List Pre-Release Sequences
The /pdb/rest/getStatusSequence service is discontinued. You can get pre-release sequences
from REST API: https://data.rcsb.org/rest/v1/holdings/unreleased?ids=450D,451D.
List Biological Assemblies
Number of biological assemblies associated with a PDB entry. Former endpoint:
/pdb/rest/bioassembly/nrbioassemblies?structureId=1hv4
GraphQL Query:
Access the transformation information needed to generate a biological assembly
(nr=0 will return information for the asymmetric unit, nr=1 will return information
for the first assembly, etc.). Former endpoint:
/pdb/rest/bioassembly/bioassembly?structureId=1hv4&nr=1
| Legacy API Field | GraphQL API Field |
|---|---|
| bioassembly.structureId | assembly.rcsb_assembly_container_identifiers.entry_id |
| bioassembly.assemblyNr | assembly.rcsb_assembly_container_identifiers.assembly_id |
| bioassembly.method | assembly.pdbx_struct_assembly.method_details |
| bioassembly.desc | assembly.pdbx_struct_assembly.details |
| transformations.chainIds | assembly.pdbx_struct_assembly_gen.asym_id_list |
| transformations.operator | assembly.pdbx_struct_oper_list.id |
|
transformations.matrix: m11, m12, m13, m21, m22, m23, m31, m32, m33 |
pdbx_struct_oper_list: matrix_1_1, matrix_1_2, matrix_1_3, matrix_2_1, matrix_2_2, matrix_2_3, matrix_3_1, matrix_3_2, matrix_3_3 |
|
transformations.shift: v1, v2, v3 |
pdbx_struct_oper_list: vector_1, vector_2, vector_3 |
GraphQL Query:
Annotations
Legacy DAS Service is discontinued. Please, find below examples similar in content.
- Third-party annotations mapped onto PDB chains
- PDB to UniProtKB mappings
- Pfam mappings for PDB
- Access Gene Ontology terms a for a PDB chain
Third-party annotations
Provides various third party annotations that have been computed for PDB chains (SCOP, CATH, etc.).
Similar in content to former endpoint: /pdb/rest/das/pdbchainfeatures/features?segment=5pti.A
GraphQL Query:
PDB to UniProtKB mappings
GraphQL Query:
Pfam annotations for PDB entries
The support of /pdb/rest/hmmer is discontinued. Pfam annotations can be requested as:
GraphQL Query:
Gene Ontology terms for PDB chains
List the Gene Ontology terms that have been annotated for a PDB chain.
(Same as on the Annotations tab in the structure explorer pages). Former endpoint:
/pdb/rest/goTerms?structureId=4HHB.A,1A4W.H
GraphQL Query:
Sequence and Structure Clusters
Sequence cluster membership of individual entities is now accessed via the
rcsb_polymer_entity_group_membership attribute:
GraphQL Query:
The rcsb_cluster_membership property should not be used anymore.
Structure clusters are not available at this point but may be added in a future release.
Contact Us
Contact info@rcsb.org with questions or feedback about this service.