› 5hjr

X-ray diffraction
2.4Å resolution

Murine endoplasmic reticulum alpha-glucosidase II with bound covalent intermediate

Released:
DOI: 10.2210/pdb5hjr/pdb
PDB entry 5hjr coloured by chain, front view.
PDB entry 5hjr coloured by chain, side view.
PDB entry 5hjr coloured by chain, top view.
Source organism: Mus musculus
Primary publication:
Structures of mammalian ER α-glucosidase II capture the binding modes of broad-spectrum iminosugar antivirals.
Caputo AT, Alonzi DS, Marti L, Reca IB, Kiappes JL, Struwe WB, Cross A, Basu S, Lowe ED, Darlot B, Santino A, Roversi P, Zitzmann N
Proc Natl Acad Sci U S A 113 E4630-8 (2016)
PMID: 27462106

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-126675 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (4 distinct):
Neutral alpha-glucosidase AB Chains: A, C
Molecule details ›
Chains: A, C
Length: 857 amino acids
Theoretical weight: 97.89 KDa
Source organism: Mus musculus
Expression system: Homo sapiens
UniProt:
  • Canonical: Q8BHN3 (Residues: 33-922; Coverage: 92%)
  • Best match: Q8BHN3-3 (Residues: 1-670)
Gene names: G2an, Ganab, Kiaa0088
Sequence domains:
Glucosidase 2 subunit beta Chains: B, D
Molecule details ›
Chains: B, D
Length: 83 amino acids
Theoretical weight: 8.91 KDa
Source organism: Mus musculus
Expression system: Homo sapiens
UniProt:
  • Canonical: O08795 (Residues: 35-117; Coverage: 16%)
Gene name: Prkcsh
Sequence domains: Glucosidase II beta subunit-like

Ligands and Environments

Carbohydrate polymer : NEW Components: NAG, BMA, MAN
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG, BMA, MAN
Carbohydrate polymer
7 bound ligands:
Ligand EDO 7 x EDO
Ligand FMT 32 x FMT
Ligand 5GF 2 x 5GF
Ligand P6G 4 x P6G
Ligand OXM 3 x OXM
Ligand TAR 1 x TAR
Ligand CA 4 x CA
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I03
Spacegroup: P21
Unit cell:
a: 103.512Å b: 174.664Å c: 63.714Å
α: 90° β: 91.31° γ: 90°
R-values:
R R work R free
0.179 0.177 0.202
Expression system: Homo sapiens

Quick links

Citations

10 review citations

Iminosugar antivirals: the therapeutic sweet spot.
Alonzi et al. (2017)
9 more

3 mentions without citation

Structures of mammalian ER α-glucosidase II capture the binding modes of broad-spectrum iminosugar antivirals.
Caputo et al. (2016)
2 more