› 8k7h

X-ray diffraction
2.28Å resolution

Crystal structure of human lysosomal alpha-galactosidase A in complex with (2R,3S,4R)-2-(hydroxymethyl)-1-methylpyrrolidine-3,4-diol

Released:
DOI: 10.2210/pdb8k7h/pdb
PDB entry 8k7h coloured by chain, front view.
PDB entry 8k7h coloured by chain, side view.
PDB entry 8k7h 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
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG, BMA, MAN
Carbohydrate polymer
3 bound ligands:
Ligand NAG 3 x NAG
Ligand VMO 2 x VMO
Ligand SO4 2 x SO4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: NSRRC BEAMLINE TPS 05A
Spacegroup: P3221
Unit cell:
a: 90.513Å b: 90.513Å c: 216.346Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.173 0.171 0.21
Expression system: Homo sapiens

Quick links