› 5lvx

X-ray diffraction
2.2Å resolution

Crystal structure of glucocerebrosidase with an inhibitory quinazoline modulator

Released:
DOI: 10.2210/pdb5lvx/pdb
PDB entry 5lvx coloured by chain, front view.
PDB entry 5lvx coloured by chain, side view.
PDB entry 5lvx coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
β-Glucocerebrosidase Modulators Promote Dimerization of β-Glucocerebrosidase and Reveal an Allosteric Binding Site.
Zheng J, Chen L, Skinner OS, Ysselstein D, Remis J, Lansbury P, Skerlj R, Mrosek M, Heunisch U, Krapp S, Charrow J, Schwake M, Kelleher NL, Silverman RB, Krainc D
J Am Chem Soc 140 5914-5924 (2018)
PMID: 29676907

Function and Biology Details

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

Structure analysis Details

Assembly composition:
homo tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-137379 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecules (4 distinct):
Lysosomal acid glucosylceramidase Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 497 amino acids
Theoretical weight: 55.66 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: P04062 (Residues: 40-536; Coverage: 100%)
Gene names: GBA, GBA1, GC, GLUC
Sequence domains:
Structure domains:

Ligands and Environments

Carbohydrate polymer : NEW Components: NAG, BMA, MAN
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG, BMA, MAN
Carbohydrate polymer
4 bound ligands:
Ligand 79B 2 x 79B
Ligand PO4 21 x PO4
Ligand NAG 2 x NAG
Ligand 7E4 2 x 7E4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SLS BEAMLINE X06SA
Spacegroup: P21
Unit cell:
a: 94.91Å b: 132.281Å c: 103.085Å
α: 90° β: 95.26° γ: 90°
R-values:
R R work R free
0.189 0.189 0.21
Expression system: Homo sapiens

Quick links

Citations

3 review citations

Evaluation of Strategies for Measuring Lysosomal Glucocerebrosidase Activity.
Ysselstein et al. (2021)
2 more

4 mentions without citation

Second-Generation Pharmacological Chaperones: Beyond Inhibitors.
Tran et al. (2020)
3 more