Crystal structure of staphylococcus aureus membrane-bound transglycosylase in complex with a lipid II analog

Structure

x-ray diffraction · 2 distinct chains · 60% helix, 1% strand (DSSP).

Ligands and binding sites

• LHI · [(2R,3R,4R,5S,6R)-4-[(2R)-1-[[(2S)-1-[2-[2-[2-[5-[(3aS,4S,6aR)-2-oxidanylidene-1,3,3a,4,6,6a-hexahydrothieno[3,4-d]imidazol-4-yl]pentanoylamino]ethoxy]ethoxy]ethylamino]-1-oxidanylidene-propan-2-yl]amino]-1-oxidanylidene-propan-2-yl]oxy-3-acetamido-5-[(2S,3R,4R,5R,6R)-3-acetamido-6-(hydroxymethyl)-4,5-bis(oxidanyl)oxan-2-yl]oxy-6-(hydroxymethyl)oxan-2-yl] [oxidanyl(3,7,11,15,19,23,27,31,35,39,43-undecamethyltetratetraconta-2,6,10,14,18,22,26,30,34,38,42-undecaenoxy)phosphoryl] hydrogen phosphate · ligand · chains A
• MG · Magnesium ion · metal · 2 copies · chains A

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 · 454 Ų buried · 6 hydrogen bonds · protein-protein

Compared structures

• 3VMT · Crystal structure of Staphylococcus aureus membrane-bound transglycosylase in complex… · the same entry in another collection · chain A against A, TM-score 1.00
• Q99T05 · AlphaFold monomer V2.0 prediction for monofunctional glycosyltransferase (Q99T05) · a predicted model of the same protein · chain A against A, TM-score 0.96

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 Q99T05
• Elsewhere: RCSB PDB 3VMT · PDBe 3VMT · UniProt Q99T05