PDB entries with extended CCD IDs
Jose Duarte
wwPDB, in collaboration with the PDBx/mmCIF Working Group, has set plans to extend the length of accession codes (IDs) for PDB and Chemical Component Dictionary (CCD) entries in the future. PDB entries containing these extended IDs will not be supported by the legacy PDB file format. (see previous announcement)
CCD
entries are currently identified by unique three-character alphanumeric
IDs. At current growth rates, we anticipate running out of
three-character IDs before 2024. After this point, the wwPDB will issue five-character alphanumeric accession codes for CCD IDs
in the OneDep system. To avoid confusion with current four-character
PDB IDs, four-character codes will not be used. Owing to limitations of
the legacy PDB file format, PDB entries containing the new five
character ID codes will only be distributed in PDBx/mmCIF format.
In addition, wwPDB has reserved a set of CCD IDs: 01 - 99, DRG, INH, LIG that will never be used in the PDB. These reserved codes can be used for new ligands during structure determination so that they can be identified as new upon deposition and added to the CCD during biocuration.
wwPDB is asking users and software developers to review their code and remove any current limitations on CCD ID lengths, and to enable use of PDBx/mmCIF format files. Example files with extended PDB and/or CCD IDs are available via github to assist code revisions, see https://github.com/wwPDB/extended-wwPDB-identifier-examples. To learn about PDBx/mmCIF, please visit https://mmcif.wwpdb.org/.
Note that all RCSB APIs will use the extended CCD ids as soon as they become available.
For any further information please contact us at in...@wwpdb.org
Best regards
RCSB Protein Data Bank