PDB Entries with Novel Ligands Now Distributed Only in PDBx/mmCIF and PDBML File Formats
The PDB three-character Chemical Component IDs are consumed and PDB has begun issuing five-character alphanumeric accession codes for CCD IDs in the OneDep system. To avoid confusion with current four-character PDB IDs, four-character codes are not used. Owing to limitations of the legacy PDB file format, PDB entries containing the new five character ID codes are distributed in PDBx/mmCIF and PDBML formats (see previous announcement).PDB entries containing these extended IDs will not be supported by the legacy PDB file format (see previous announcement).
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 PDB and CCD ID lengths, and to enable use of PDBx/mmCIF format files. https://github.com/wwPDB/extended-wwPDB-identifier-examplesExample files with extended PDB and/or CCD IDs are available via GitHub to assist with code revisions To learn about PDBx/mmCIF, please visit https://mmcif.wwpdb.org/.
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