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

Prefix

pdb

Alternative Prefixes

pdbe RCSB_PDB pdbj 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

• 2024 FURNA: A database for functional annotations of RNA structures
• 2021 Protein Data Bank Japan: Celebrating our 20th anniversary during a global pandemic as the Asian hub of three dimensional macromolecular structural data
• 2017 New tools and functions in data-out activities at Protein Data Bank Japan (PDBj)
• 2016 Protein Data Bank Japan (PDBj): updated user interfaces, resource description framework, analysis tools for large structures
• 2011 Protein Data Bank Japan (PDBj): maintaining a structural data archive and resource description framework format
• 2011 Protein Data Bank Japan (PDBj): an interview with Haruki Nakamura of Osaka University by Wendy A. Warr
• 2010 PDBj Mine: design and implementation of relational database interface for Protein Data Bank Japan
• 2002 [Development of PDBj: Advanced database for protein structures]

A summary of the relations in the Bioregistry schema can be found here.

Provided By

pdbsum validatordb viperdb

In Collection

Resources mentioned in "Sharing biological data: why, when, and how" ChEBI Data Sources Global Biodata Coalition - Global Core Biodata Resources

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.

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

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

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.

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