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Annotation of Protein Modifications in the PDB

10/08 wwPDB News

The PDB archive is now including annotation of protein chemical modifications (PCMs) and post-translational modifications (PTMs) in a standardized way.

As previously announced, the PDBx/mmCIF dictionary has been extended to enhance PCM and PTM annotation.

This includes new PDBx/mmCIF categories and items as follows:

In the Chemical Component Definition (CCD) files:

  • A new item in the chem_comp category: chem_comp.pdbx_pcm, stating whether the CCD is a known PCM/PTM.
  • A new category called pdbx_chem_comp_pcm, stating the PCM/PTM 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 PTM accession ID.

In the atomic coordinate files:

Additionally to providing this new annotation, any protein modifications that are inconsistently handled within PDB entries are amended, to ensure that a given modification is consistently handled in the PDB archive. This includes a major clean-up of incorrect link records (struct_conn).

All entries containing protein modifications are being re-released gradually from October 2024, throughout Spring 2025.

This standardization ensures that there is a single approach to handling each protein modification that occurs within the PDB archive, allowing better findability.

Questions or feedback? Contact deposit-help@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 at EMBL-EBI, and is funded by BBSRC grant number BB/V018779/1.

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