› 8k7j

X-ray diffraction
2.01Å resolution

Crystal structure of human lysosomal alpha-galactosidase A in complex with (2R,3R,4S,5R)-2-((dimethylamino)methyl)-5-(hydroxymethyl)pyrrolidine-3,4-diol

Released:
DOI: 10.2210/pdb8k7j/pdb
PDB entry 8k7j coloured by chain, front view.
PDB entry 8k7j coloured by chain, side view.
PDB entry 8k7j coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Mechanistic Insights into Dibasic Iminosugars as pH-Selective Pharmacological Chaperones to Stabilize Human α-Galactosidase.
Li HY, Lin HY, Chang SK, Chiu YT, Hou CC, Ko TP, Huang KF, Niu DM, Cheng WC
JACS Au 4 908-918 (2024)
PMID: 38559739

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:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-138990 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecules (3 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: Homo sapiens
UniProt:
  • Canonical: P06280 (Residues: 32-429; Coverage: 100%)
Gene name: GLA
Sequence domains:

Ligands and Environments

Carbohydrate polymer : NEW Components: NAG, BMA, MAN
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG
Carbohydrate polymer
4 bound ligands:
Ligand NAG 1 x NAG
Ligand VNB 2 x VNB
Ligand SO4 5 x SO4
Ligand P6G 1 x P6G
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: NSRRC BEAMLINE TPS 05A
Spacegroup: P3221
Unit cell:
a: 90.677Å b: 90.677Å c: 216.331Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.158 0.157 0.191
Expression system: Homo sapiens

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