› 5npf

X-ray diffraction
1.38Å resolution

Crystal structure of txGH116 (beta-glucosidase from Thermoanaerobacterium xylolyticum) in complex with beta Cyclophellitol Cyclosulfate probe ME594

Released:
DOI: 10.2210/pdb5npf/pdb
PDB entry 5npf coloured by chain, front view.
PDB entry 5npf coloured by chain, side view.
PDB entry 5npf coloured by chain, top view.
Source organism: Thermoanaerobacterium xylanolyticum
Primary publication:
1,6-Cyclophellitol Cyclosulfates: A New Class of Irreversible Glycosidase Inhibitor.
Artola M, Wu L, Ferraz MJ, Kuo CL, Raich L, Breen IZ, Offen WA, Codée JDC, van der Marel GA, Rovira C, Aerts JMFG, Davies GJ, Overkleeft HS
OpenAccess logo ACS Cent Sci 3 784-793 (2017)
PMID: 28776021

Function and Biology Details

Reaction catalysed: 
D-glucosyl-N-acylsphingosine + H(2)O = D-glucose + N-acylsphingosine
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-514549 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Glucosylceramidase Chain: A
Molecule details ›
Chain: A
Length: 798 amino acids
Theoretical weight: 91.72 KDa
Source organism: Thermoanaerobacterium xylanolyticum
Expression system: Escherichia coli
UniProt:
  • Canonical: F6BL85 (Residues: 19-806; Coverage: 98%)
Gene name: Thexy_2211
Sequence domains:

Ligands and Environments

3 bound ligands:
Ligand EDO 13 x EDO
Ligand CA 1 x CA
Ligand 945 1 x 945
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I02
Spacegroup: P21212
Unit cell:
a: 178.18Å b: 53.81Å c: 83.3Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.127 0.125 0.16
Expression system: Escherichia coli

Quick links

Citations

28 citation in other articles

Dynamic and Functional Profiling of Xylan-Degrading Enzymes in Aspergillus Secretomes Using Activity-Based Probes.
Schröder et al. (2019)
27 more