Dear all,
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
<https://www.wwpdb.org/news/news?year=2023#64bff95ed78e004e766a9687>,
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 ourdocumentation
<https://www.wwpdb.org/documentation/peptides-remediation>, 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.
Questions or feedback? contactdeposit-h...@mail.wwpdb.org.
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 byPDBe
<https://www.ebi.ac.uk/pdbe/>atEMBL-EBI <https://www.ebi.ac.uk/>, and is
funded by BBSRC grant number BB/V018779/1.
Kind regards,
Deborah Harrus, on behalf of the wwPDB
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Deborah Harrus, Ph.D.
PDBe Archive Project Leader, Biocuration Lead
PDBe - Protein Data Bank in Europe
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD UK
http://www.PDBe.org
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