› 2w92

X-ray diffraction
1.65Å resolution

Structure of a Streptococcus pneumoniae family 85 glycoside hydrolase, Endo-D, in complex with NAG-thiazoline.

Released:
DOI: 10.2210/pdb2w92/pdb
PDB entry 2w92 coloured by chain, front view.
PDB entry 2w92 coloured by chain, side view.
PDB entry 2w92 coloured by chain, top view.
Source organism: Streptococcus pneumoniae TIGR4
Primary publication:
Streptococcus pneumoniae endohexosaminidase D, structural and mechanistic insight into substrate-assisted catalysis in family 85 glycoside hydrolases.
Abbott DW, Macauley MS, Vocadlo DJ, Boraston AB
J Biol Chem 284 11676-89 (2009)
PMID: 19181667

Function and Biology Details

Biochemical function:
Biological process:
  • not assigned
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-188064 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Endo-beta-N-acetylglucosaminidase D Chain: A
Molecule details ›
Chain: A
Length: 653 amino acids
Theoretical weight: 73.59 KDa
Source organism: Streptococcus pneumoniae TIGR4
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q93HW0 (Residues: 159-807; Coverage: 40%)
Gene name: Endo D
Sequence domains: Glycosyl hydrolase family 85
Structure domains:

Ligands and Environments

2 bound ligands:
Ligand 1PE 1 x 1PE
Ligand NGT 1 x NGT
No modified residues

Experiments and Validation Details

Entry percentile scores
Spacegroup: C2
Unit cell:
a: 134.88Å b: 59.04Å c: 96.5Å
α: 90° β: 110.25° γ: 90°
R-values:
R R work R free
0.149 0.147 0.187
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

10 review citations

Glycosidase inhibition: assessing mimicry of the transition state.
Gloster et al. (2010)
9 more

6 mentions without citation

Sculpting therapeutic monoclonal antibody N-glycans using endoglycosidases.
Trastoy et al. (2022)
5 more