1x3w

X-ray diffraction
3Å resolution

Structure of a peptide:N-glycanase-Rad23 complex

Released:

Function and Biology Details

Reaction catalysed:
Hydrolysis of an N(4)-(acetyl-beta-D-glucosaminyl)asparagine residue in which the glucosamine residue may be further glycosylated, to yield a (substituted) N-acetyl-beta-D-glucosaminylamine and a peptide containing an aspartate residue
Biochemical function:
Cellular component:

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
PDBe Complex ID:
PDB-CPX-152412 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (3 distinct):
Peptide-N(4)-(N-acetyl-beta-glucosaminyl)asparagine amidase Chain: A
Molecule details ›
Chain: A
Length: 335 amino acids
Theoretical weight: 39.57 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q02890 (Residues: 8-342; Coverage: 92%)
Gene names: PNG1, YPL096W
Sequence domains: Transglutaminase-like superfamily
Structure domains:
UV excision repair protein RAD23 Chain: B
Molecule details ›
Chain: B
Length: 72 amino acids
Theoretical weight: 7.54 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P32628 (Residues: 238-309; Coverage: 18%)
Gene names: RAD23, SYGP-ORF29, YEL037C
Sequence domains: XPC-binding domain
Structure domains: XPC-binding domain

Ligands and Environments

Carbohydrate polymer : NEW Components: GLC, FRU
1 bound ligand:
1 modified residue:

Experiments and Validation Details

Entry percentile scores
X-ray source: PHOTON FACTORY BEAMLINE BL-5A
Spacegroup: P3121
Unit cell:
a: 129.235Å b: 129.235Å c: 128.494Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.245 0.244 0.274
Expression system: Escherichia coli BL21(DE3)