Crystal structure of human lysosomal acid-alpha-glucosidase, gaa, in complex with N-hydroxyethyl-1-deoxynojirimycin

Structure

x-ray diffraction · 1 distinct chain · 22% helix, 30% strand (DSSP).

Ligands and binding sites

• MIG · (2R,3R,4R,5S)-1-(2-hydroxyethyl)-2-(hydroxymethyl) piperidine-3,4,5-triol · ligand · chains A
• NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 9 copies · chains A
• FUC · alpha-L-fucopyranose · sugar · 2 copies · chains A
• BMA · beta-D-mannopyranose · sugar
• SO4 · Sulfate ion · ion · 5 copies · chains A
• CL · Chloride ion · ion · 3 copies · chains A
• EDO · 1,2-ethanediol · additive · 13 copies · chains A
• PGE · Triethylene glycol · additive · 4 copies · chains A
• GOL · Glycerol · additive · 3 copies · chains A

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

Pockets

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

Modifications

Observed in the structure: 5 disulfide, 5 glycan, 1 modified (disulfide, N-glycosylation, oxidation).

Compared structures

• 5NN6 · Crystal structure of human lysosomal acid-alpha-glucosidase, GAA, in complex with… · the same entry in another collection · chain A against A, TM-score 1.00
• P10253 · AlphaFold monomer V2.0 prediction for lysosomal alpha-glucosidase (P10253) · 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 P10253
• Elsewhere: RCSB PDB 5NN6 · PDBe 5NN6 · UniProt P10253