› 6z3i

X-ray diffraction
1.8Å resolution

Structure of recombinant beta-glucocerebrosidase in complex with bifunctional cyclophellitol aziridine activity based probe

Released:
DOI: 10.2210/pdb6z3i/pdb
PDB entry 6z3i coloured by chain, front view.
PDB entry 6z3i coloured by chain, side view.
PDB entry 6z3i 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:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-137377 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecules (2 distinct):
Lysosomal acid glucosylceramidase Chain: BBB
Molecule details ›
Chain: BBB
Length: 497 amino acids
Theoretical weight: 55.66 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: P04062 (Residues: 40-536; Coverage: 100%)
Gene names: GBA, GBA1, GC, GLUC
Sequence domains:

Ligands and Environments

Carbohydrate polymer : NEW Components: NAG, BMA, MAN
Carbohydrate polymer
4 bound ligands:
Ligand SO4 4 x SO4
Ligand NAG 2 x NAG
Ligand EDO 16 x EDO
Ligand Q68 1 x Q68
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I04
Spacegroup: P21
Unit cell:
a: 53.139Å b: 76.67Å c: 67.988Å
α: 90° β: 102.053° γ: 90°
R-values:
R R work R free
0.179 0.178 0.189
Expression system: Trichoplusia ni

Quick links

Citations

3 citation in other articles

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