X-ray structure of acid-beta-glucosidase with 5N,6S-(N'-(N-octyl) imino)-6-thionojirimycin in the active site

Structure

x-ray diffraction · 2 distinct chains · 27% helix, 27% strand (DSSP).

Ligands and binding sites

• AMF · (3Z,5S,6R,7S,8R,8aS)-3-(octylimino)hexahydro[1,3]thiazolo[3,4-a]pyridine-5,6,7,8-tetrol · ligand · 2 copies · chains A, B
• NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, B
• BMA · beta-D-mannopyranose · sugar · 2 copies
• FUC · alpha-L-fucopyranose · sugar · 2 copies
• K · Potassium ion · metal · 2 copies · chains A, B
• PO4 · Phosphate ion · ion · 2 copies · chains A, B

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

Pockets

7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Interfaces

1 interface between chains.

• A–B · 902 Ų buried · 3 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide, 2 glycan (disulfide, N-glycosylation).

Compared structures

• 2XWE · X-ray structure of acid-beta-glucosidase with 5N,6S-(N'-(N-OCTYL)IMINO)-6-thionojirimycin… · the same entry in another collection · chain A against A, TM-score 1.00
• P04062 · AlphaFold monomer V2.0 prediction for lysosomal acid glucosylceramidase (P04062) · a predicted model of the same protein · chain A against A, TM-score 1.00

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 P04062
• Elsewhere: RCSB PDB 2XWE · PDBe 2XWE · UniProt P04062