[3dem] Coming Soon: PDB Entries with Novel Ligands Distributed Only in PDBx/mmCIF and PDBML File Formats
Justin Flatt
justin at rcsb.rutgers.edu
Mon Sep 18 10:00:38 PDT 2023
At current growth rates, we anticipate running out of three-character
Chemical Component IDs by the end of 2023. 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 and PDBML formats (see
previous announcement [1]).
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 asks users and software developers to review code to remove any
current limitations on CCD ID lengths, and to enable use of PDBx/mmCIF
format files. Example files with extended CCD IDs are available via
GitHub [2] to assist code revisions. Information about the PDBx/mmCIF
dictionary and file format is provided at mmcif.wwpdb.org [3].
For any further information please contact us at info at wwpdb.org.
Links:
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[1] https://urldefense.com/v3/__http://www.wwpdb.org/news/news?year=2023*63ff72ccc031758bf1c30ff7__;Iw!!Mih3wA!BMXihq7zM1PCcHAQxDWcebMdn-i6YMD4ihZXYAMaFHxUqj2FDMnr4rzJQ425YPbfp0w1VgCl2LJuZ9Ldd2yjdwnh$
[2] https://urldefense.com/v3/__https://github.com/wwPDB/extended-wwPDB-identifier-examples__;!!Mih3wA!BMXihq7zM1PCcHAQxDWcebMdn-i6YMD4ihZXYAMaFHxUqj2FDMnr4rzJQ425YPbfp0w1VgCl2LJuZ9Ldd5H7JLNo$
[3] https://urldefense.com/v3/__https://mmcif.wwpdb.org/__;!!Mih3wA!BMXihq7zM1PCcHAQxDWcebMdn-i6YMD4ihZXYAMaFHxUqj2FDMnr4rzJQ425YPbfp0w1VgCl2LJuZ9Ldd8Vpc-SE$
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