Backbone Annotation and Standardization of Peptide Residues is Now Live
The wwPDB has rolled 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 have been updated accordingly. This improves the Findability and Interoperability of the PDB data and opens up new opportunities to use the updated peptide residue annotation.
As announced previously, new data items have been added 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 have been 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 have standardized the atom nomenclature of peptide backbone atoms in CCD files to follow a standard convention. This follows a set of rules, outlined in our documentation, ensuring that atom nomenclature for carboxyl groups, amino groups and side chain linked carbons (C-alpha) follow a standard atom nomenclature. This allows clear identification of backbone atoms for peptide residues across the whole archive.
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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.