Wbpe, an aminotransferase from pseudomonas aeruginosa involved in O- antigen assembly in complex with product as the external aldimine

Structure

x-ray diffraction · 1 distinct chain · 41% helix, 16% strand (DSSP).

Ligands and binding sites

• UD0 · (2S,3S,4R,5R,6R)-5-(acetylamino)-6-{[(S)-{[(S)-{[(2S,3R,4S,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methoxy}(hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]oxy}-3-hydroxy-4-{[(1E)-{3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene]amino}tetrahydro-2H-pyran-2-carboxylic acid · ligand · 2 copies · chains A, B
• SO4 · Sulfate ion · ion · chains A
• GOL · Glycerol · additive · chains A, B

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

Pockets

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

Interfaces

1 interface between chains.

• A–B · 2233 Ų buried · 38 hydrogen bonds · protein-protein

Compared structures

• 3NUB · WbpE, an Aminotransferase from Pseudomonas aeruginosa Involved in O-antigen Assembly in… · the same entry in another collection · chain A against A, TM-score 1.00
• Q9HZ76 · AlphaFold monomer V2.0 prediction for udp-2-acetamido-2-deoxy-3-oxo- D-glucuronate… · 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 Q9HZ76
• Elsewhere: RCSB PDB 3NUB · PDBe 3NUB · UniProt Q9HZ76