› 7kad

X-ray diffraction
2.51Å resolution

Co-crystal structure of alpha glucosidase with compound 6

Released:
DOI: 10.2210/pdb7kad/pdb
PDB entry 7kad coloured by chain, front view.
PDB entry 7kad coloured by chain, side view.
PDB entry 7kad coloured by chain, top view.
Source organism: Mus musculus
Primary publication:
N-Substituted Valiolamine Derivatives as Potent Inhibitors of Endoplasmic Reticulum α-Glucosidases I and II with Antiviral Activity.
Karade SS, Hill ML, Kiappes JL, Manne R, Aakula B, Zitzmann N, Warfield KL, Treston AM, Mariuzza RA
J Med Chem 64 18010-18024 (2021)
PMID: 34870992

Function and Biology Details

Reaction catalysed: 
Glc(2)Man(9)GlcNAc(2)-[protein] + H(2)O = GlcMan(9)GlcNAc(2)-[protein] + beta-D-glucopyranose
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-126674 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Neutral alpha-glucosidase AB Chains: A, C
Molecule details ›
Chains: A, C
Length: 977 amino acids
Theoretical weight: 110.65 KDa
Source organism: Mus musculus
Expression system: Homo sapiens
UniProt:
  • Canonical: Q8BHN3 (Residues: 33-187, 188-944; Coverage: 100%)
  • Best match: Q8BHN3-3 (Residues: 1-692)
Gene names: G2an, Ganab, Kiaa0088
Sequence domains:
Glucosidase 2 subunit beta Chains: B, D
Molecule details ›
Chains: B, D
Length: 554 amino acids
Theoretical weight: 62.31 KDa
Source organism: Mus musculus
Expression system: Homo sapiens
UniProt:
  • Canonical: O08795 (Residues: 15-517; Coverage: 99%)
Gene name: Prkcsh
Sequence domains:

Ligands and Environments

7 bound ligands:
Ligand W9Y 2 x W9Y
Ligand EDO 33 x EDO
Ligand PGE 6 x PGE
Ligand PEG 13 x PEG
Ligand SO4 13 x SO4
Ligand CA 4 x CA
Ligand PG4 1 x PG4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 23-ID-B
Spacegroup: P32
Unit cell:
a: 102.689Å b: 102.689Å c: 240.275Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.173 0.172 0.203
Expression system: Homo sapiens

Quick links

Citations

2 review citations

Beyond the vaccines: a glance at the small molecule and peptide-based anti-COVID19 arsenal.
Nepali et al. (2022)
1 more