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› 5ief

X-ray diffraction
2.38Å resolution

Murine endoplasmic reticulum alpha-glucosidase II with N-butyl-1-deoxynojirimycin

Released:
DOI: 10.2210/pdb5ief/pdb
Model geometry
Fit model/data
PDB entry 5ief coloured by chain, front view.
PDB entry 5ief coloured by chain, side view.
PDB entry 5ief 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: 
(1) N(4)-(alpha-D-Glc-(1->3)-alpha-D-Glc-(1->3)-alpha-D-Man-(1->2)-alpha-D-Man-(1->2)-alpha-D-Man-(1->3)-[alpha-D-Man-(1->2)-alpha-D-Man-(1->3)-[alpha-D-Man-(1->2)-alpha-D-Man-(1->6)]-alpha-D-Man-(1->6)]-beta-D-Man-(1->4)-beta-D-GlcNAc-(1->4)-beta-D-GlcNAc)-L-asparaginyl-[protein] +H2O = N(4)-(alpha-D-Glc-(1->3)-alpha-D-Man-(1->2)-alpha-D-Man-(1->2)-alpha-D-Man-(1->3)-[alpha-D-Man-(1->2)-alpha-D-Man-(1->3)-[alpha-D-Man-(1->2)-alpha-D-Man-(1->6)]-alpha-D-Man-(1->6)]-beta-D-Man-(1->4)-beta-D-GlcNAc-(1->4)-beta-D-GlcNAc)-L-asparaginyl-[protein] + beta-D-glucose.
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 (3 distinct):
Neutral alpha-glucosidase AB Chain: A
Molecule details ›
Chain: A
Length: 913 amino acids
Theoretical weight: 103.73 KDa
Source organism: Mus musculus
Expression system: Homo sapiens
UniProt:
  • Canonical: Q8BHN3 (Residues: 33-944; Coverage: 100%)
Gene names: G2an, Ganab, Kiaa0088
Sequence domains:
Glucosidase 2 subunit beta Chain: B
Molecule details ›
Chain: B
Length: 88 amino acids
Theoretical weight: 9.57 KDa
Source organism: Mus musculus
Expression system: Homo sapiens
UniProt:
  • Canonical: O08795 (Residues: 30-117; Coverage: 17%)
Gene name: Prkcsh
Sequence domains: Glucosidase II beta subunit-like

Ligands and Environments

Carbohydrate polymer : NEW Components: NAG
Carbohydrate polymer
5 bound ligands:
Ligand FMT 1 x FMT
Ligand ACT 1 x ACT
Ligand NBV 1 x NBV
Ligand P6G 2 x P6G
Ligand CA 2 x CA
No modified residues

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: ESRF BEAMLINE BM14
Spacegroup: P21212
Unit cell:
a: 103.84Å b: 172.89Å c: 62.77Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.188 0.186 0.218
Expression system: Homo sapiens

Quick links

Citations

9 review citations

Medicinal chemistry strategies toward host targeting antiviral agents.
Ji et al. (2020)
8 more

4 mentions without citation

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