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

• 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].

Provided By

pdbsum validatordb

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

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.

Additional providers curated in the Bioregistry are listed here.