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Future Planning: Entries with extended PDB and CCD ID codes will be distributed in PDBx/mmCIF format only

04/20 wwPDB News

wwPDB, in collaboration with the PDBx/mmCIF Working Group, has set plans to extend the length of ID codes for PDB and Chemical Component Dictionary (CCD) ID entries in the future. Entries containing these extended IDs will not be supported by the legacy PDB file format.

CCD entries are currently identified by unique three-character alphanumeric codes. At current growth rates, we anticipate running out of available new codes in the next three to four years. At this point, the wwPDB will issue four-character alphanumeric codes for CCD IDs in the OneDep system. Due to constraints of the legacy PDB file format, entries containing these new, four character ID codes will only be distributed in PDBx/mmCIF format. The wwPDB will begin implementation of extended CCD ID codes in 2022.


In addition, wwPDB also plans to extend PDB ID length to eight characters prefixed by ‘PDB’, e.g., pdb_00001abc. Each PDB ID has a corresponding Digital Object Identifier (DOI), often required for manuscript submission to journals and described in publications by the structure authors. Both extended PDB IDs and corresponding PDB DOIs, along with existing four character PDB IDs, will be included in the PDBx/mmCIF formatted files for all new entries by Fall 2021.

For example, PDB entry 1ABC will also have the extended PDB ID (pdb_00001abc) and the corresponding PDB DOI (10.2210/pdb1abc/pdb) listed in the _database_2 PDBx/mmCIF category.

PDB 1abc pdb_00001abc 10.2210/pdb1abc/pdb
WWPDB D_1xxxxxxxxx ? ?

Once four-character PDB IDs are all consumed, newly-deposited PDB entries will only be issued extended PDB ID codes, and entries will only be distributed in PDBx/mmCIF format.

wwPDB is asking PDB users and related software developers to review code and begin to remove such limitations for the future.

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