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

Structure

x-ray diffraction · 2 distinct chains · 20% helix, 30% strand (DSSP).

Ligands and binding sites

• NBV · (2R,3R,4R,5S)-1-butyl-2-(hydroxymethyl)piperidine-3,4,5-triol · ligand · chains A
• NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A
• CA · Calcium ion · metal · 2 copies · chains A, B
• P6G · Hexaethylene glycol · additive · 2 copies · chains A
• FMT · Formic acid · additive · chains A
• ACT · Acetate ion · additive · chains A

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

10 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Interfaces

1 interface between chains.

• A–B · 752 Ų buried · 16 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 7 disulfide, 1 glycan (disulfide, N-glycosylation).

Compared structures

• 5IEF · Murine endoplasmic reticulum alpha-glucosidase II with N-butyl-1-deoxynojirimycin · the same entry in another collection · chain A against A, TM-score 1.00
• Q8BHN3 · AlphaFold monomer V2.0 prediction for neutral alpha-glucosidase ab (Q8BHN3) · a predicted model of the same protein · chain A against A, TM-score 1.00
• O08795 · AlphaFold monomer V2.0 prediction for glucosidase 2 subunit beta (O08795) · a predicted model of the same protein · chain B against A, TM-score 0.91

Analyse

• Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
• Every structure of UniProt Q8BHN3
• Every structure of UniProt O08795
• Elsewhere: RCSB PDB 5IEF · PDBe 5IEF · UniProt Q8BHN3 · UniProt O08795