› 2oyk

X-ray diffraction
1.5Å resolution

Endo-glycoceramidase II from Rhodococcus sp.: cellobiose-like isofagomine complex

Released:
DOI: 10.2210/pdb2oyk/pdb
PDB entry 2oyk coloured by chain, front view.
PDB entry 2oyk coloured by chain, side view.
PDB entry 2oyk coloured by chain, top view.
Source organism: Rhodococcus sp.
Primary publication:
The structural basis of glycosidase inhibition by five-membered iminocyclitols: the clan a glycoside hydrolase endoglycoceramidase as a model system.
Caines ME, Hancock SM, Tarling CA, Wrodnigg TM, Stick RV, Stütz AE, Vasella A, Withers SG, Strynadka NC
Angew Chem Int Ed Engl 46 4474-6 (2007)
PMID: 17487923

Function and Biology Details

Reaction catalysed: 
Oligoglycosylglucosyl-(1<->1)-ceramide + H(2)O = ceramide + oligoglycosylglucose
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-128508 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Endoglycoceramidase II Chains: A, B
Molecule details ›
Chains: A, B
Length: 481 amino acids
Theoretical weight: 52.12 KDa
Source organism: Rhodococcus sp.
Expression system: Escherichia coli
UniProt:
  • Canonical: O33853 (Residues: 31-490; Coverage: 99%)
Sequence domains:
Structure domains:

Ligands and Environments

3 bound ligands:
Ligand NA 4 x NA
Ligand 9MR 2 x 9MR
Ligand GOL 1 x GOL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ALS BEAMLINE 8.2.2
Spacegroup: P21
Unit cell:
a: 53.545Å b: 92.919Å c: 94.489Å
α: 90° β: 98.32° γ: 90°
R-values:
R R work R free
0.178 0.177 0.198
Expression system: Escherichia coli

Quick links

Citations

10 citation in other articles

Five-membered iminocyclitol α-glucosidase inhibitors: synthetic, biological screening and in silico studies.
Guerreiro et al. (2013)
9 more