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

Prefix
pdb
Alternative Prefixes
pdbe pdbj RCSB_PDB wwpdb
Keywords
bioinformatics epidemiology protein proteomics structural biology structure virology
Links
Homepage
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
Metaregistry PDB Structure

The metaregistry provides mappings between the Bioregistry and other registries. There are 14 mappings to external registries for this resource with 9 unique external prefixes.

Registry Name Registry Metaprefix External Prefix Curate
BioContext biocontext PDB
EDAM EDAM Ontology logo edam 1127
FAIRSharing FAIRSharing logo fairsharing FAIRsharing.rs2815
GO Gene Ontology Registry logo go PDB
Integbio Integbio logo integbio nbdc00613
Identifiers.org Identifiers.org logo miriam pdb
N2T Name-to-Thing logo n2t pdb
NCBI National Center for Biotechnology Information Registry logo ncbi PDB
Pathguide Pathguide logo pathguide 398
Prefix Commons Prefix Commons logo prefixcommons pdbj
re3data Registry of Research Data Repositories logo re3data r3d100010910
TogoID togoid Pdb
UniProt UniProt Cross-ref database logo uniprot DB-0172
Wikidata Wikidata Property logo wikidata P638
RDF Information

When using this resource in RDF, the following URI format should be used:

https://rdf.wwpdb.org/pdb/$1

Providers

A provider turns a local unique identifiers from a resource into a URI. Many providers are also resolvable as URLs (i.e., they can be used in a web browser).

The local unique identifier 2gc4 is used to demonstrate the providers available for PDB Structure. A guide for curating additional providers can be found here.

Name Metaprefix URI
PDB Structure pdb https://www.wwpdb.org/pdb?id=2gc4
PDB Structure (RDF) rdf https://rdf.wwpdb.org/pdb/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
Extra Providers

Additional providers curated in the Bioregistry are listed here. These are typically inherited from Identifiers.org or Prefix Commons, and need extra curation.

Code Name URL
CURATOR_REVIEW Proteopedia http://proteopedia.org/wiki/index.php/2gc4
bio2rdf Bio2RDF http://bio2rdf.org/pdbj: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