The Protein Data Bank is the single worldwide archive of structural data of biological macromolecules.

Prefix
pdb
Alternative Prefixes
RCSB_PDB pdbe pdbj wwpdb
Keywords
bioinformatics epidemiology protein proteomics structural biology structure virology
Links
Homepage @PDBj_en
Contact
Haruki Nakamura   0000-0001-6690-5863
Pattern for Local Unique Identifiers

Local identifiers in PDB Structure should match this regular expression:
^[0-9][A-Za-z0-9]{3}$

Example Local Unique Identifier
2gc4   Resolve
Pattern for CURIES

Compact URIs (CURIEs) constructed from PDB Structure should match this regular expression:
^pdb:[0-9][A-Za-z0-9]{3}$

Example CURIE
pdb:2gc4
Publications
Ontology
Metaregistry PDB Structure

The metaregistry provides mappings between the Bioregistry and other registries. There are 11 mappings to external registries for pdb with 7 unique external prefixes.

Registry Name Registry Metaprefix External Prefix Curate
BioContext biocontext PDB
EDAM Ontology edam 1127
FAIRSharing FAIRSharing logo fairsharing FAIRsharing.rs2815
Gene Ontology Registry go PDB
Identifiers.org Identifiers.org logo miriam pdb
Name-to-Thing Name-to-Thing logo n2t pdb
National Center for Biotechnology Information Registry ncbi PDB
Prefix Commons prefixcommons pdbj
Registry of Research Data Repositories re3data r3d100010910
UniProt Cross-ref database uniprot DB-0172
Wikidata Property Wikidata Property logo wikidata P638
Providers

Providers are various services that resolve CURIEs to URLs. The example CURIE pdb:2gc4 is used to demonstrate the provides available for pdb. Generation of OLS and BioPortal URLs requires additional programmatic logic beyond string formatting.

Name Metaprefix URI
PDB Structure pdb https://www.wwpdb.org/pdb?id=2gc4
Bioregistry bioregistry https://bioregistry.io/pdb:2gc4
Identifiers.org miriam https://identifiers.org/pdb:2gc4
Name-to-Thing n2t https://n2t.net/pdb:2gc4
None CURATOR_REVIEW http://proteopedia.org/wiki/index.php/2gc4
None ebi https://www.ebi.ac.uk/pdbsum/2gc4
None pdbe https://www.ebi.ac.uk/pdbe/entry/pdb/2gc4
None pdbj https://pdbj.org/mine/summary/2gc4
None rcsb https://www.rcsb.org/structure/2gc4
Extra Providers

Additional providers curated in the Bioregistry are listed here.

Code Name URL
CURATOR_REVIEW Proteopedia http://proteopedia.org/wiki/index.php/2gc4
ebi Protein Databank through PDBsum https://www.ebi.ac.uk/pdbsum/2gc4
pdbe Protein Databank in Europe (PDBe) https://www.ebi.ac.uk/pdbe/entry/pdb/2gc4
pdbj Protein Data Bank Japan (PDBj) https://pdbj.org/mine/summary/2gc4
rcsb RCSB PDB https://www.rcsb.org/structure/2gc4