[3dem] Coming soon: Annotation of Protein Modifications in the PDB

[Justin Flatt]

The standardization of protein modification handling ensures that there 
is a single correct approach to handling each protein modification that 
occurs within the PDB archive. However, there are many existing PDB 
entries that contain protein modifications which do not follow these 
handling conventions.

As part of the protein modifications remediation project, all model 
coordinates files containing protein modifications are being re-released 
to add a new protein modification data category. This new category will 
list all observed PCMs/PTMs within the entry, as well as their type and 
category, allowing better findability.

A new category will also be added to the Chemical Component Definition 
(CCD) files. It will state whether the CCD is a known PCM, its type and 
category, as well as on which positions in the amino acid and in the 
polypeptide it is expected to be observed. If this PCM is also a known 
PTM, it will have the Uniprot generic PTM accession ID.

Finally, any protein modifications that are inconsistently handled 
within a PDB entry will be amended, to ensure that a given modification 
is consistently handled in the PDB archive.

Detailed information about this work is available from GitHub, including 
PDBx/mmCIF dictionary extension and a set of example files, and complete 
documentation of the additional annotation 
<https://urldefense.com/v3/__https://github.com/wwPDB/protein-modification-extension__;!!Mih3wA!F-KOj-PHGD50QRG1N9KnUDV4LNMdsEvWgxMILyBcNvJCud6NGjp6QNIDdB33mQX_gl_6vvDQtqxRa5BKJW78LNfJ$ >.

Questions or feedback? Contact deposit-help at mail.wwpdb.org. 
<mailto:deposit-help at mail.wwpdb.org>

The protein chemical modifications (PCMs) and post translational 
modifications (PTMs) remediation project is a wwPDB collaborative 
project carried out principally by PDBe <https://urldefense.com/v3/__https://www.ebi.ac.uk/pdbe/__;!!Mih3wA!F-KOj-PHGD50QRG1N9KnUDV4LNMdsEvWgxMILyBcNvJCud6NGjp6QNIDdB33mQX_gl_6vvDQtqxRa5BKJc-4u-vY$ > at 
EMBL-EBI <https://urldefense.com/v3/__https://www.ebi.ac.uk/__;!!Mih3wA!F-KOj-PHGD50QRG1N9KnUDV4LNMdsEvWgxMILyBcNvJCud6NGjp6QNIDdB33mQX_gl_6vvDQtqxRa5BKJTigZOZ8$ >, and is funded by BBSRC grant number 
BB/V018779/1.

See full news at 
https://urldefense.com/v3/__http://www.wwpdb.org/news/news?year=2024*662fa1a565d8a8cacaf76f9c__;Iw!!Mih3wA!F-KOj-PHGD50QRG1N9KnUDV4LNMdsEvWgxMILyBcNvJCud6NGjp6QNIDdB33mQX_gl_6vvDQtqxRa5BKJVwso8Xs$ 
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