Dear all,
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 and will not be
supported by the legacy PDB file format (see previous announcement
<https://www.wwpdb.org/news/news?year=2023#63ff72ccc031758bf1c30ff7>).
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. Example files with extended PDB and/or
CCD IDs are available via GitHub
<https://github.com/wwPDB/extended-wwPDB-identifier-examples>to assist
with code revisions.
To learn about PDBx/mmCIF, please visit https://mmcif.wwpdb.org/
<https://www.wwpdb.org/news/mmcif.wwpdb.org/>.
For any further information please contact us at [email protected]
Kind regards,
Deborah Harrus, on behalf of the wwPDB
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Deborah Harrus, Ph.D.
PDBe Archive Project Leader, Biocuration Lead
PDBe - Protein Data Bank in Europe
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD UK
http://www.PDBe.org
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