› 2vc9

X-ray diffraction
2.36Å resolution

Family 89 Glycoside Hydrolase from Clostridium perfringens in complex with 2-acetamido-1,2-dideoxynojirmycin

Released:
DOI: 10.2210/pdb2vc9/pdb
PDB entry 2vc9 coloured by chain, front view.
PDB entry 2vc9 coloured by chain, side view.
PDB entry 2vc9 coloured by chain, top view.
Source organism: Clostridium perfringens
Primary publication:
Structural and mechanistic insight into the basis of mucopolysaccharidosis IIIB.
Ficko-Blean E, Stubbs KA, Nemirovsky O, Vocadlo DJ, Boraston AB
Proc Natl Acad Sci U S A 105 6560-5 (2008)
PMID: 18443291

Function and Biology Details

Reaction catalysed: 
Hydrolysis of terminal non-reducing N-acetyl-D-glucosamine residues in N-acetyl-alpha-D-glucosaminides
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-101683 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Alpha-N-acetylglucosaminidase family protein Chain: A
Molecule details ›
Chain: A
Length: 891 amino acids
Theoretical weight: 102.27 KDa
Source organism: Clostridium perfringens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: A0A0H2YU91 (Residues: 26-916; Coverage: 43%)
Gene name: CPF_0859
Sequence domains:
Structure domains:

Ligands and Environments

3 bound ligands:
Ligand NOK 1 x NOK
Ligand GOL 2 x GOL
Ligand CA 1 x CA
No modified residues

Experiments and Validation Details

Entry percentile scores
Spacegroup: P61
Unit cell:
a: 90.96Å b: 90.96Å c: 252.4Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.205 0.203 0.246
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

10 review citations

Mechanistic insights into glycosidase chemistry.
Vocadlo et al. (2008)
9 more

2 mentions without citation

Structural and mechanistic insight into the basis of mucopolysaccharidosis IIIB.
Ficko-Blean et al. (2008)
1 more