Co-crystal structure of alpha glucosidase with compound 11

Structure

x-ray diffraction · 3 distinct chains · 20% helix, 31% strand (DSSP).

Ligands and binding sites

• X8Y · (1S,2S,3R,4S,5S)-5-({6-[(4-azido-2-nitrophenyl) amino]hexyl}amino)-1-(hydroxymethyl)cyclohexane-1,2,3, 4-tetrol · ligand · 2 copies · chains A, C
• CA · Calcium ion · metal · 4 copies · chains A, B, C, D
• SO4 · Sulfate ion · ion · 2 copies · chains A, C
• EDO · 1,2-ethanediol · additive · 5 copies · chains A, C
• PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains A, C
• P6G · Hexaethylene glycol · additive · chains A, C

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

Pockets

20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.

Interfaces

3 interfaces between chains.

• A–C · 880 Ų buried · 20 hydrogen bonds · protein-protein
• A–B · 743 Ų buried · 19 hydrogen bonds · protein-protein
• C–D · 740 Ų buried · 20 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 14 disulfide, 1 covalent (disulfide, additive adduct).

Compared structures

• 7KRY · Co-crystal structure of alpha glucosidase with compound 11 · the same entry in another collection · chain D against D, TM-score 1.00
• Q8BHN3 · AlphaFold monomer V2.0 prediction for neutral alpha-glucosidase ab (Q8BHN3) · a predicted model of the same protein · chain C 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 D against A, TM-score 0.95

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 7KRY · PDBe 7KRY · UniProt Q8BHN3 · UniProt O08795