[3dem] Backbone Annotation and Standardization of Peptide Residues is Now Live
Justin Flatt
justin at rcsb.rutgers.edu
Mon Nov 27 07:02:43 PST 2023
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 [1], 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 [2], 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.
_Updated peptide CCDs will have standardized atom names and backbone /
N- and C- terminal annotation._
Questions or feedback? Contact deposit-help at 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 [3] at EMBL-EBI
[4], and is funded by BBSRC grant number BB/V018779/1.
Links:
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[1] https://urldefense.com/v3/__http://www.wwpdb.org/news/news?year=2023*64bff95ed78e004e766a9687__;Iw!!Mih3wA!G3dpeB_s6LT7s6UWaZUFfaf5FjeNdsSZlftYSWzLpJt0IrXYqLpykyscb3sSsPGiVpb0En8GKBmvQnNzsp6SCKQ_$
[2] https://urldefense.com/v3/__http://www.wwpdb.org/documentation/peptides-remediation__;!!Mih3wA!G3dpeB_s6LT7s6UWaZUFfaf5FjeNdsSZlftYSWzLpJt0IrXYqLpykyscb3sSsPGiVpb0En8GKBmvQnNzsqWVksk0$
[3] https://urldefense.com/v3/__https://www.ebi.ac.uk/pdbe/__;!!Mih3wA!G3dpeB_s6LT7s6UWaZUFfaf5FjeNdsSZlftYSWzLpJt0IrXYqLpykyscb3sSsPGiVpb0En8GKBmvQnNzsuyXIfgW$
[4] https://urldefense.com/v3/__https://www.ebi.ac.uk/__;!!Mih3wA!G3dpeB_s6LT7s6UWaZUFfaf5FjeNdsSZlftYSWzLpJt0IrXYqLpykyscb3sSsPGiVpb0En8GKBmvQnNzstf00Py2$
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