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Updated Annotation and Standardization of Peptide Residues

07/25 wwPDB News

In October 2023, the wwPDB will roll out updated Chemical Component Dictionary (CCD) data files with standardized atom naming and additional annotation of protein backbone and terminal atoms within peptide residues. Entries containing those updated CCDs will also be updated accordingly. This will improve the Findability and Interoperability of the PDB data, as well as open up new opportunities to use the updated peptide residue annotation.

As part of this remediation process, we will add new data items to the CCD files for peptide-linking components to label atoms that form the backbone, N- or C-terminal groups. Three new CCD data items will be added to the CCD category _chem_comp_atom as pdbx_backbone_flag, pdbx_n-terminal_flag and pdbx_c-terminal_flag, flagging the backbone, N-terminal and C-terminal atoms, respectively.

Furthermore, we will be standardizing the atom nomenclature of peptide backbone atoms in CCD files to follow a standard convention. This will follow a set of rules, outlined in the documentation linked below, ensuring that atom nomenclature for carboxyl groups, amino groups and side chain linked carbons (C-alpha) follow a standard atom nomenclature. This will allow clear identification of backbone atoms for peptide residues across the whole archive.

Detailed information about this work is available from the wwPDB website, including PDBx/mmCIF dictionary extension and example files (GitHub; Peptide Residues Chemical Component Dictionary Remediation Documentation).

<I>Updated peptide CCDs will have standardized atom names and backbone / N- and C- terminal annotation.</I>Updated peptide CCDs will have standardized atom names and backbone / N- and C- terminal annotation.

We encourage developers of software packages for refinement or visualization of PDB data to review this information.

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The peptide residues chemical component dictionary remediation project is part of the protein chemical modifications (PCMs) and post translational modifications (PTMs) remediation project, 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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