PDBe 2ydr

X-ray diffraction
2.75Å resolution

CpOGA D298N in complex with p53-derived O-GlcNAc peptide

Released:

Function and Biology Details

Reaction catalysed:
[Protein]-3-O-(N-acetyl-beta-D-glucosaminyl)-L-serine + H(2)O = [protein]-L-serine + N-acetyl-D-glucosamine
Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
O-GlcNAcase NagJ Chain: A
Molecule details ›
Chain: A
Length: 590 amino acids
Theoretical weight: 66.13 KDa
Source organism: Clostridium perfringens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q0TR53 (Residues: 31-618; Coverage: 61%)
Gene names: CPF_1442, nagJ
Sequence domains:
Structure domains:
Cellular tumor antigen p53 Chain: P
Molecule details ›
Chain: P
Length: 11 amino acids
Theoretical weight: 1.2 KDa
Source organism: Homo sapiens
Expression system: Not provided
UniProt:
  • Canonical: P04637 (Residues: 144-154; Coverage: 3%)
Gene names: P53, TP53

Ligands and Environments

2 bound ligands:

No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I03
Spacegroup: P61
Unit cell:
a: 117.95Å b: 117.95Å c: 148.121Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.186 0.185 0.219
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided