› 3vkk

X-ray diffraction
2Å resolution

Crystal Structure Of The Covalent Intermediate Of Human Cytosolic Beta-Glucosidase-mannose complex

Released:
DOI: 10.2210/pdb3vkk/pdb
PDB entry 3vkk coloured by chain, front view.
PDB entry 3vkk coloured by chain, side view.
PDB entry 3vkk coloured by chain, top view.
Source organism: Homo sapiens
Entry authors: Noguchi J, Hayashi Y, Okino N, Ito M, Kimura M, Kakuta Y

Function and Biology Details

Reactions catalysed: 
Hydrolysis of terminal, non-reducing beta-D-glucosyl residues with release of beta-D-glucose
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-190531 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Cytosolic beta-glucosidase Chain: A
Molecule details ›
Chain: A
Length: 469 amino acids
Theoretical weight: 53.75 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9H227 (Residues: 1-469; Coverage: 100%)
Gene names: CBG, CBGL1, GBA3
Sequence domains: Glycosyl hydrolase family 1
Structure domains: Glycosidases

Ligands and Environments

6 bound ligands:
Ligand GOL 3 x GOL
Ligand CL 2 x CL
Ligand PLM 1 x PLM
Ligand OLA 1 x OLA
Ligand MAN 1 x MAN
Ligand MG 1 x MG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL38B1
Spacegroup: P212121
Unit cell:
a: 65.733Å b: 83.519Å c: 90.892Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.184 0.182 0.222
Expression system: Escherichia coli

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