› 2vur

X-ray diffraction
2.2Å resolution

Chemical dissection of the link between Streptozotocin, O-GlcNAc and pancreatic cell death

Released:
DOI: 10.2210/pdb2vur/pdb
PDB entry 2vur coloured by chain, front view.
PDB entry 2vur coloured by chain, side view.
PDB entry 2vur coloured by chain, top view.
Source organism: Clostridium perfringens
Primary publication:
Chemical dissection of the link between streptozotocin, O-GlcNAc, and pancreatic cell death.
Pathak S, Dorfmueller HC, Borodkin VS, van Aalten DM
Chem Biol 15 799-807 (2008)
PMID: 18721751

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
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-171162 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
O-GlcNAcase NagJ Chains: A, B
Molecule details ›
Chains: A, B
Length: 594 amino acids
Theoretical weight: 66.69 KDa
Source organism: Clostridium perfringens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q0TR53 (Residues: 31-624; Coverage: 61%)
Gene names: CPF_1442, nagJ
Sequence domains:
Structure domains:

Ligands and Environments

2 bound ligands:
Ligand YX1 2 x YX1
Ligand SO4 1 x SO4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID14-4
Spacegroup: I212121
Unit cell:
a: 130.47Å b: 149.731Å c: 152.121Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.196 0.195 0.241
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

6 review citations

The hexosamine signaling pathway: O-GlcNAc cycling in feast or famine.
Hanover et al. (2010)
5 more

2 mentions without citation

Screening-based discovery of drug-like O-GlcNAcase inhibitor scaffolds.
Dorfmueller et al. (2010)
1 more