Crystal structure of wlard, a sugar 3N-formyl transferase in the presence of dtpd-QUI3N, dtdp-QUI3NFO, and thf

Structure

x-ray diffraction · 2 distinct chains · 26% helix, 27% strand (DSSP).

Ligands and binding sites

• 1YJ · N-[4-({[(6R)-2-amino-4-oxo-3,4,5,6,7,8-hexahydropteridin-6-yl]methyl}amino)benzoyl]-L-glutamic acid · ligand · 2 copies · chains A, B
• T3Q · [(3R,4S,5S,6R)-4-amino-3,5-dihydroxy-6-methyloxan-2-yl][hydroxy-[[(2R,3S,5R)-3-hydroxy-5-(5-methyl-2,4-dioxopyrimidin-1-yl)oxolan-2-yl]methoxy]phosphoryl] hydrogen phosphate · ligand · chains A
• 1YF · [(2R,3R,4S,5S,6R)-4-formamido-6-methyl-3,5-bis(oxidanyl)oxan-2-yl] [[(2R,3S,5R)-5-[5-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] hydrogen phosphate · ligand · chains B
• MPO · 3[N-morpholino]propane sulfonic acid · additive · 2 copies · chains A, B

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

Pockets

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

Interfaces

1 interface between chains.

• A–B · 1284 Ų buried · 20 hydrogen bonds · protein-protein

Compared structures

• 4LY3 · Crystal structure of WlaRD, a sugar 3N-formyl transferase in the presence of dTPD-Qui3N… · the same entry in another collection · chain B against B, 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 A8FMJ3
• Elsewhere: RCSB PDB 4LY3 · PDBe 4LY3 · UniProt A8FMJ3