Coming soon: Annotation of Protein Modifications in the PDB

04/30 wwPDB News


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.

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The protein chemical modifications (PCMs) and post translational modifications (PTMs) remediation project is a wwPDB collaborative project carried out principally by PDBe at EMBL-EBI, and is funded by BBSRC grant number BB/V018779/1.

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