› 6ytr

X-ray diffraction
1.7Å resolution

Structure of recombinant human beta-glucocerebrosidase in complex with cyclophellitol aziridine inhibitor

Released:
DOI: 10.2210/pdb6ytr/pdb
PDB entry 6ytr coloured by chain, front view.
PDB entry 6ytr coloured by chain, side view.
PDB entry 6ytr 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 (4 distinct):
Lysosomal acid glucosylceramidase Chains: AAA, BBB
Molecule details ›
Chains: AAA, 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
Carbohydrate polymer : NEW Components: NAG, BMA
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG
Carbohydrate polymer
5 bound ligands:
Ligand PO8 2 x PO8
Ligand SO4 7 x SO4
Ligand NAG 1 x NAG
Ligand EDO 42 x EDO
Ligand NA 2 x NA
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I02
Spacegroup: P21
Unit cell:
a: 53.155Å b: 156.779Å c: 68.23Å
α: 90° β: 102.116° γ: 90°
R-values:
R R work R free
0.161 0.159 0.203
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