› 7k9t

X-ray diffraction
2.1Å resolution

Co-crystal structure of alpha glucosidase with compound 5

Released:
DOI: 10.2210/pdb7k9t/pdb
PDB entry 7k9t coloured by chain, front view.
PDB entry 7k9t coloured by chain, side view.
PDB entry 7k9t 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

Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-106544 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Alpha glucosidase 2 alpha neutral subunit 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: A1A4T2 (Residues: 33-966; Coverage: 100%)
Gene name: Ganab
Sequence domains:
Glucosidase 2 subunit beta Chains: B, D
Molecule details ›
Chains: B, D
Length: 547 amino acids
Theoretical weight: 61.45 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

8 bound ligands:
Ligand W9V 2 x W9V
Ligand PGE 9 x PGE
Ligand PEG 12 x PEG
Ligand EDO 25 x EDO
Ligand SO4 6 x SO4
Ligand CA 4 x CA
Ligand PG4 2 x PG4
Ligand P6G 1 x P6G
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 23-ID-B
Spacegroup: P32
Unit cell:
a: 102.87Å b: 102.87Å c: 240.653Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.171 0.171 0.192
Expression system: Homo sapiens

Quick links

Citations

3 review citations

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