› 3thd

X-ray diffraction
1.79Å resolution

Crystal structure of human beta-galactosidase in complex with 1-deoxygalactonojirimycin

Released:
DOI: 10.2210/pdb3thd/pdb
PDB entry 3thd coloured by chain, front view.
PDB entry 3thd coloured by chain, side view.
PDB entry 3thd coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Crystal structure of human β-galactosidase: structural basis of Gm1 gangliosidosis and morquio B diseases.
Ohto U, Usui K, Ochi T, Yuki K, Satow Y, Shimizu T
J Biol Chem 287 1801-12 (2012)
PMID: 22128166

Function and Biology Details

Reaction catalysed: 
Hydrolysis of terminal non-reducing beta-D-galactose residues in beta-D-galactosides
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-147669 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Beta-galactosidase Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 654 amino acids
Theoretical weight: 73.67 KDa
Source organism: Homo sapiens
Expression system: Komagataella pastoris
UniProt:
  • Canonical: P16278 (Residues: 24-677; Coverage: 100%)
Gene names: ELNR1, GLB1
Sequence domains:
Structure domains:

Ligands and Environments

5 bound ligands:
Ligand NAG 16 x NAG
Ligand CL 4 x CL
Ligand DGJ 4 x DGJ
Ligand SO4 8 x SO4
Ligand EDO 8 x EDO
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: PHOTON FACTORY BEAMLINE AR-NW12A
Spacegroup: P21
Unit cell:
a: 94.792Å b: 115.996Å c: 140.327Å
α: 90° β: 92.22° γ: 90°
R-values:
R R work R free
0.199 0.198 0.228
Expression system: Komagataella pastoris

Quick links

Citations

12 review citations

Ganglioside biochemistry.
Kolter T. (2012)
11 more

7 mentions without citation

Crystal structure of human β-galactosidase: structural basis of Gm1 gangliosidosis and morquio B diseases.
Ohto et al. (2012)
6 more