› 4nxs

X-ray diffraction
2.55Å resolution

Crystal structure of human alpha-galactosidase A in complex with 1-deoxygalactonojirimycin-pFPhT

Released:
DOI: 10.2210/pdb4nxs/pdb
PDB entry 4nxs coloured by chain, front view.
PDB entry 4nxs coloured by chain, side view.
PDB entry 4nxs coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Molecular basis of 1-deoxygalactonojirimycin arylthiourea binding to human α-galactosidase a: pharmacological chaperoning efficacy on Fabry disease mutants.
Yu Y, Mena-Barragán T, Higaki K, Johnson JL, Drury JE, Lieberman RL, Nakasone N, Ninomiya H, Tsukimura T, Sakuraba H, Suzuki Y, Nanba E, Mellet CO, García Fernández JM, Ohno K
ACS Chem Biol 9 1460-9 (2014)
PMID: 24783948

Function and Biology Details

Reaction catalysed: 
Hydrolysis of terminal, non-reducing alpha-D-galactose residues in alpha-D-galactosides, including galactose oligosaccharides, galactomannans and galactolipids
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-138990 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecules (2 distinct):
Alpha-galactosidase A Chains: A, B
Molecule details ›
Chains: A, B
Length: 398 amino acids
Theoretical weight: 45.39 KDa
Source organism: Homo sapiens
Expression system: Cricetulus griseus
UniProt:
  • Canonical: P06280 (Residues: 32-429; Coverage: 100%)
Gene name: GLA
Sequence domains:
Structure domains:

Ligands and Environments

Carbohydrate polymer : NEW Components: NAG
Carbohydrate polymer
3 bound ligands:
Ligand SO4 5 x SO4
Ligand NAG 4 x NAG
Ligand 2OZ 2 x 2OZ
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 22-ID
Spacegroup: P3221
Unit cell:
a: 90.783Å b: 90.783Å c: 217.382Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.19 0.187 0.232
Expression system: Cricetulus griseus

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Citations

6 review citations

Pharmacological Chaperones: A Therapeutic Approach for Diseases Caused by Destabilizing Missense Mutations.
Liguori et al. (2020)
5 more

2 mentions without citation

Crystal Structure and Mutational Analysis of Isomalto-dextranase, a Member of Glycoside Hydrolase Family 27.
Okazawa et al. (2015)
1 more