type in ['L-peptide linking', 'L-peptide COOH carboxy terminus', 'L-peptide NH3 amino terminus']
pdbx_ambiguous_flag == N
pdbx_release_status == REL
code: three_letter_code
id: three_letter_code
name: name
synonyms: SYSTEMATIC NAME
parent: one_letter_code
structure: SMILES_CANONICAL
dbPTM: website down
Delta Mass: no structures provided
FindMod: uses UniProt vocabulary
PDB in Europe Chemical Components: same as PDB Chemical Components
PSIMOD: no structures
UniMod: no structures
UniProt Controlled Vocabulary of Posttranslational Modifications: defined in terms of RESID and PSI-MI
Result
We converted all PDB-CCD entries to residues (removed OH from the C terminus) to be consistent with RESID
Merging PDB-CCD with RESID added 915 additional monomeric forms that are not in RESID
128 PDB-CCD entries have the same structures as RESID entries
38 of these are connections are not annotated in RESID
38 RESID entries are annotated with PDB-CCD entries that have different structures (generally different sterochemistry or bond orders). Nevertheless, we merged these entries. The merged entries use the RESID structure.
jonrkarr
commented
5 years ago
Done
DNA
No merging necessary because there's only one database.
RNA
Merged MODOMICS and the RNA Modification Database. This added two additional monomers.
Protein
Plan
dbPTM: website downDelta Mass: no structures providedFindMod: uses UniProt vocabularyPDB in Europe Chemical Components: same as PDB Chemical ComponentsPSIMOD: no structuresUniMod: no structuresUniProt Controlled Vocabulary of Posttranslational Modifications: defined in terms of RESID and PSI-MIResult