Co-crystal structure of alpha glucosidase with compound 3

Structure

x-ray diffraction · 4 distinct chains · 19% helix, 30% strand (DSSP).

Ligands and binding sites

• W9P · (1~{S},2~{S},3~{R},4~{S},5~{S})-1-(hydroxymethyl)-5-[6-[[2-[oxidanyl(oxidanylidene)-$L^{4}-azanyl]-4-(1,2,3, 4-tetrazol-1-yl)phenyl]amino]hexylamino]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 · chains A, C
• EDO · 1,2-ethanediol · additive · 27 copies · chains A, B, C, D
• PEG · Di(hydroxyethyl)ether · additive · 4 copies · chains A, C, D
• PGE · Triethylene glycol · additive · 3 copies · 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, 8 with a druggability of 0.5 or more.

Interfaces

3 interfaces between chains.

• A–C · 875 Ų buried · 26 hydrogen bonds · protein-protein
• A–B · 741 Ų buried · 18 hydrogen bonds · protein-protein
• C–D · 738 Ų buried · 16 hydrogen bonds · protein-protein

Modifications

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

Compared structures

• 7K9O · Co-crystal structure of alpha glucosidase with compound 3 · the same entry in another collection · 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 0.96

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 A1A4T2
• Every structure of UniProt O08795
• Elsewhere: RCSB PDB 7K9O · PDBe 7K9O · UniProt A1A4T2 · UniProt O08795