We've built a new version of this page with an interactive 3D viewer. Try it out in beta and help us improve:

› 5abg

X-ray diffraction
2Å resolution

Structure of GH84 with ligand

Released:
DOI: 10.2210/pdb5abg/pdb
Model geometry
Fit model/data
PDB entry 5abg coloured by chain, front view.
PDB entry 5abg coloured by chain, side view.
PDB entry 5abg coloured by chain, top view.
Source organism: Bacteroides thetaiotaomicron
Primary publication:
A Convenient Approach to Stereoisomeric Iminocyclitols: Generation of Potent Brain-Permeable OGA Inhibitors.
Bergeron-Brlek M, Goodwin-Tindall J, Cekic N, Roth C, Zandberg WF, Shan X, Varghese V, Chan S, Davies GJ, Vocadlo DJ, Britton R
Angew Chem Int Ed Engl 54 15429-33 (2015)
PMID: 26545827

Function and Biology Details

Reaction catalysed: 
[(1) 3-O-(N-acetyl-beta-D-glucosaminyl)-L-seryl-[protein] + H2O =N-acetyl-D-glucosamine + L-seryl-[protein]., (2) 3-O-(N-acetyl-beta-D-glucosaminyl)-L-threonyl-[protein] + H2O =L-threonyl-[protein] + N-acetyl-D-glucosamine., (1) 3-O-(N-acetyl-beta-D-glucosaminyl)-L-seryl-[protein] + H2O =N-acetyl-D-glucosamine + L-seryl-[protein]., (2) 3-O-(N-acetyl-beta-D-glucosaminyl)-L-threonyl-[protein] + H2O =L-threonyl-[protein] + N-acetyl-D-glucosamine.]
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-183580 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
O-GlcNAcase BT_4395 Chains: A, B
Molecule details ›
Chains: A, B
Length: 726 amino acids
Theoretical weight: 83.51 KDa
Source organism: Bacteroides thetaiotaomicron
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q89ZI2 (Residues: 22-737; Coverage: 100%)
Gene name: BT_4395
Sequence domains:
Structure domains:

Ligands and Environments

3 bound ligands:
Ligand EDO 2 x EDO
Ligand V0N 2 x V0N
Ligand CA 1 x CA
No modified residues

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: DIAMOND BEAMLINE I04
Unit cell:
a: 51.531Å b: 161.184Å c: 223.98Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.206 0.204 0.235
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

6 review citations

Advances in chemical probing of protein O-GlcNAc glycosylation: structural role and molecular mechanisms.
Saha et al. (2021)
5 more