Crystal structure of mouse xyloside xylosyltransferase 1 complexed with manganese, product ligand and udp (product complex II)

Structure

x-ray diffraction · 2 distinct chains · 42% helix, 18% strand (DSSP).

Ligands and binding sites

• UDP · Uridine-5'-diphosphate · ligand · chains A
• XYS · alpha-D-xylopyranose · sugar · 2 copies · chains A
• BGC · beta-D-glucopyranose · sugar · chains A, D
• MN · Manganese (II) ion · metal · chains A
• SO4 · Sulfate ion · ion · chains A

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

Pockets

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

Interfaces

1 interface between chains.

• A–D · 639 Ų buried · 5 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 5 disulfide, 1 glycan (disulfide, O-glycosylation).

Compared structures

• 4WMK · Crystal structure of mouse Xyloside xylosyltransferase 1 complexed with manganese… · the same entry in another collection · chain A against A, TM-score 1.00
• Q3U4G3 · AlphaFold monomer V2.0 prediction for xyloside xylosyltransferase 1 (Q3U4G3) · a predicted model of the same protein · chain A against A, TM-score 1.00
• P00740 · AlphaFold monomer V2.0 prediction for coagulation factor IX (P00740) · a predicted model of the same protein · chain D against A, TM-score 0.43

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 Q3U4G3
• Every structure of UniProt P00740
• Elsewhere: RCSB PDB 4WMK · PDBe 4WMK · UniProt Q3U4G3 · UniProt P00740