Crystal structure of human alpha-galactosidase a in complex with alpha-galactose configured cyclosulfamidate ME763

Structure

x-ray diffraction · 2 distinct chains · 32% helix, 25% strand (DSSP).

Ligands and binding sites

• YTW · (3~{A}~{R},4~{S},5~{S},6~{S},7~{R},7~{A}~{S})-7-(hydroxymethyl)-2,2-bis(oxidanylidene)-3~{A},4,5,6,7, 7~{A}-hexahydro-3~{H}-benzo[d][1,2,3]oxathiazole-4,5, 6-triol · ligand · 2 copies · chains A, B
• NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 11 copies · chains A, B
• BMA · beta-D-mannopyranose · sugar · 3 copies
• MAN · alpha-D-mannopyranose · sugar · 3 copies · chains B
• SO4 · Sulfate ion · ion · 11 copies · chains A, B
• EDO · 1,2-ethanediol · additive · 12 copies · chains A, B
• PEG · Di(hydroxyethyl)ether · additive · 5 copies · chains A, B
• ACT · Acetate ion · additive · 3 copies · chains A, B

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

Pockets

1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.

Interfaces

1 interface between chains.

• A–B · 998 Ų buried · 16 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 10 disulfide, 6 glycan (disulfide, N-glycosylation).

Compared structures

• 6IBK · Crystal structure of human alpha-galactosidase A in complex with alpha-galactose… · the same entry in another collection · chain A against A, TM-score 1.00
• P06280 · AlphaFold monomer V2.0 prediction for alpha-galactosidase a (P06280) · 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 P06280
• Elsewhere: RCSB PDB 6IBK · PDBe 6IBK · UniProt P06280