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Protein Data Bank (PDB) Archive: a new architecture (beta) for scalable, PDBx/mmCIF-based data distribution
Zukang Feng1, Balakumaran Balasubramaniyan2, Gert Jan Bekker3
1RCSB Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, New Jersey, USA.
Acta Crystallographica. Section D, Structural Biology
|July 17, 2026
Summary
The Protein Data Bank (PDB) is updating its accession codes from four characters to 12 characters due to the exhaustion of current codes. This change, effective July 21st, 2027, will enhance PDB entry detection in literature.
Area of Science:
- Structural Biology
- Bioinformatics
- Data Archiving
Background:
- The Protein Data Bank (PDB) archive is rapidly expanding.
- Current four-character PDB accession codes (PDB IDs) are projected to be exhausted by 2028.
- This necessitates a change in the PDB ID format to accommodate future growth.
Purpose of the Study:
- To announce and explain the transition to a new, extended PDB ID format.
- To facilitate the robust detection of PDB entries in scientific literature.
- To encourage the adoption of the PDBx/mmCIF format alongside the new PDB IDs.
Main Methods:
- Revision of PDB accession codes to a 12-character format, prepended with `pdb_`.
- Introduction of a PDB Beta Archive to host entries with extended PDB IDs.
- Reorganization of the PDB archive files to mirror the new entry-level structure.
Main Results:
- Extended PDB IDs (e.g., pdb_1000axyz) will be implemented.
- The PDB will exclusively release entries with extended PDB IDs from July 21st, 2027.
- The PDB Beta Archive is available for community adaptation.
Conclusions:
- The PDB is transitioning to a 12-character PDB ID system to ensure long-term sustainability.
- Early adoption of the new PDB ID and PDBx/mmCIF format is encouraged.
- The PDB Beta Archive serves as a crucial resource during this transition phase.
