Crystal structure of 3-O-sulfotransferase isoform 3 in complex with 8MER oligosaccharide with 6S sulfation

Structure

x-ray diffraction · 2 distinct chains · 42% helix, 15% strand (DSSP).

Ligands and binding sites

• NPO · P-nitrophenol · ligand · 2 copies · chains B, A
• A3P · Adenosine-3'-5'-diphosphate · ligand · 2 copies · chains B, A
• NGY · 2-acetamido-2-deoxy-6-O-sulfo-alpha-D-glucopyranose · ligand · chains B, A
• SGN · 2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose · sugar · 6 copies · chains A, B
• IDS · 2-O-sulfo-alpha-L-idopyranuronic acid · sugar · 4 copies · chains A, B
• BDP · beta-D-glucopyranuronic acid · sugar · 3 copies · chains A, B
• NA · Sodium ion · metal · 2 copies · chains B, A
• EDO · 1,2-ethanediol · additive · 7 copies · chains B, A

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

Pockets

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

Interfaces

1 interface between chains.

• B–A · 1256 Ų buried · 18 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 disulfide (disulfide).

Compared structures

• 6XKG · Crystal structure of 3-O-Sulfotransferase isoform 3 in complex with 8mer oligosaccharide… · the same entry in another collection · chain B against B, TM-score 1.00
• Q9Y663 · AlphaFold monomer V2.0 prediction for heparan sulfate glucosamine 3-O-sulfotransferase… · a predicted model of the same protein · chain A against A, TM-score 0.99

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 Q9Y663
• Elsewhere: RCSB PDB 6XKG · PDBe 6XKG · UniProt Q9Y663