new cif fields (Annotation of Protein Modifications in the PDB)

[jamesmkrieger]

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:

A new item in the pdbx_entry_details category: pdbx_entry_details.has_protein_modification, stating if the entry contains a PCM/PTM.
A new category called pdbx_modification_feature, providing an instance-level annotation of all observed PCMs/PTMs within the entry, as well as their type and category.
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.