› 6z39

X-ray diffraction
1.7Å resolution

Structure of recombinant human beta-glucocerebrosidase in complex with BODIPY functionalised epoxide activity based probe

Released:
DOI: 10.2210/pdb6z39/pdb
PDB entry 6z39 coloured by chain, front view.
PDB entry 6z39 coloured by chain, side view.
PDB entry 6z39 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Design, Synthesis and Structural Analysis of Glucocerebrosidase Imaging Agents.
Rowland RJ, Chen Y, Breen I, Wu L, Offen WA, Beenakker TJ, Su Q, van den Nieuwendijk AMCH, Aerts JMFG, Artola M, Overkleeft HS, Davies GJ
Chemistry 27 16377-16388 (2021)
PMID: 34570911

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 dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-137378 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecules (2 distinct):
Lysosomal acid glucosylceramidase Chains: AAA, BBB
Molecule details ›
Chains: AAA, BBB
Length: 497 amino acids
Theoretical weight: 55.64 KDa
Source organism: Homo sapiens
Expression system: Cricetulus griseus
UniProt:
  • Canonical: P04062 (Residues: 40-536; Coverage: 100%)
Gene names: GBA, GBA1, GC, GLUC
Sequence domains:

Ligands and Environments

Carbohydrate polymer : NEW Components: NAG
Carbohydrate polymer
8 bound ligands:
Ligand NAG 2 x NAG
Ligand Q65 1 x Q65
Ligand K35 2 x K35
Ligand SO4 13 x SO4
Ligand EDO 16 x EDO
Ligand GOL 6 x GOL
Ligand GAI 1 x GAI
Ligand ACT 1 x ACT
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I03
Spacegroup: C2221
Unit cell:
a: 111.172Å b: 285.622Å c: 91.564Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.163 0.163 0.18
Expression system: Cricetulus griseus

Quick links

Citations

3 citation in other articles

Design, Synthesis and Structural Analysis of Glucocerebrosidase Imaging Agents.
Rowland et al. (2021)
2 more