Crystal structure of vlde, the pseudo-glycosyltransferase, in complex with GDP and validoxylamine a 7'-phosphate

Structure

x-ray diffraction · 2 distinct chains · 45% helix, 22% strand (DSSP).

Ligands and binding sites

• GDP · Guanosine-5'-diphosphate · ligand · 2 copies · chains A, B
• VDO · [(1R,2R,3S,4S,5S)-2,3,4-trihydroxy-5-{[(1S,4R,5S,6S)-4,5,6-trihydroxy-3-(hydroxymethyl)cyclohex-2-en-1-yl]amino}cyclohexyl]methyl dihydrogen phosphate · ligand · 2 copies · chains A, B
• CL · Chloride ion · ion · 2 copies · chains A, B
• EDO · 1,2-ethanediol · additive · 2 copies · chains A, B

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

Pockets

8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Interfaces

1 interface between chains.

• A–B · 2160 Ų buried · 62 hydrogen bonds · protein-protein

Compared structures

• 4F97 · Crystal Structure of VldE, the pseudo-glycosyltransferase, in complex with GDP and… · the same entry in another collection · chain A against A, TM-score 1.00
• Q15JG1 · AlphaFold monomer V2.0 prediction for validamine 7-phosphate valienyltransferase (Q15JG1) · a predicted model of the same protein · chain B 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 Q15JG1
• Elsewhere: RCSB PDB 4F97 · PDBe 4F97 · UniProt Q15JG1