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
http://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 our documentation
http://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? Contact deposit-help@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 by PDBe
https://www.ebi.ac.uk/pdbe/ at EMBL-EBI https://www.ebi.ac.uk/, and
is funded by BBSRC grant number BB/V018779/1.
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Regards,
Jasmine
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Jasmine Young, Ph.D.
Biocuration Team Lead
RCSB Protein Data Bank
Research Professor
Institute for Quantitative Biomedicine
Rutgers, The State University of New Jersey
174 Frelinghuysen Rd
Piscataway, NJ 08854-8087
Email:jasmine@rcsb.rutgers.edu
Phone: (848)445-0103 ext 4920
Fax: (732)445-4320
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