› 2xpk

X-ray diffraction
2.4Å resolution

Cell-penetrant, nanomolar O-GlcNAcase inhibitors selective against lysosomal hexosaminidases

Released:
DOI: 10.2210/pdb2xpk/pdb
PDB entry 2xpk coloured by chain, front view.
PDB entry 2xpk coloured by chain, side view.
PDB entry 2xpk coloured by chain, top view.
Source organism: Clostridium perfringens
Primary publication:
Cell-penetrant, nanomolar O-GlcNAcase inhibitors selective against lysosomal hexosaminidases.
Dorfmueller HC, Borodkin VS, Schimpl M, Zheng X, Kime R, Read KD, van Aalten DM
OpenAccess logo Chem Biol 17 1250-5 (2010)
PMID: 21095575

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:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-171164 (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

1 bound ligand:
Ligand Z0M 2 x Z0M
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE BM14
Spacegroup: I212121
Unit cell:
a: 130.145Å b: 144.97Å c: 153.061Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.196 0.196 0.242
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

13 review citations

Protein O-GlcNAcylation in diabetes and diabetic complications.
Ma et al. (2013)
12 more

1 mention without citation

O-GlcNAcase Fragment Discovery with Fluorescence Polarimetry.
Borodkin et al. (2018)