Crystal structure of plasmodium dxr in complex with a pyridine- containing inhibitor

Structure

x-ray diffraction · 2 distinct chains · 49% helix, 15% strand (DSSP).

Ligands and binding sites

• NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · 2 copies · chains A, B
• FOB · [(1R)-3-[acetyl(hydroxy)amino]-1-(pyridin-4-yl)propyl]phosphonic acid · ligand · 2 copies · chains A, B
• FOQ · [(1S)-3-[acetyl(hydroxy)amino]-1-(pyridin-4-yl)propyl]phosphonic acid · ligand · 2 copies · chains A, B
• MN · Manganese (II) ion · metal · 4 copies · chains A, B
• CL · Chloride ion · ion · chains A, B
• EDO · 1,2-ethanediol · additive · 3 copies · chains A, B
• ACT · Acetate ion · additive · 2 copies · chains A, B

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

Pockets

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

Interfaces

1 interface between chains.

• A–B · 2016 Ų buried · 35 hydrogen bonds · protein-protein

Compared structures

• 4GAE · Crystal structure of plasmodium dxr in complex with a pyridine-containing inhibitor · the same entry in another collection · chain A against A, TM-score 1.00
• O96693 · AlphaFold monomer V2.0 prediction for 1-deoxy-D-xylulose 5-phosphate reductoisomerase… · a predicted model of the same protein · chain B against A, TM-score 0.99

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 O96693
• Elsewhere: RCSB PDB 4GAE · PDBe 4GAE · UniProt O96693