Structure of plasmodium falciparum dxr in complex with a beta- substituted fosmidomycin analogue, LC57 and manganese

Structure

x-ray diffraction · 1 distinct chain · 51% helix, 15% strand (DSSP).

Ligands and binding sites

• LC7 · [(2R)-5-(3-fluorophenyl)-2-{2-[hydroxy(methyl)amino]-2-oxoethyl}pentyl]phosphonic acid · ligand · 2 copies · chains A, B
• 6LB · 4-ethylmorpholine · ligand · 2 copies · chains A, B
• MN · Manganese (II) ion · metal · 2 copies · chains A, B
• EDO · 1,2-ethanediol · additive · 15 copies · chains A, B
• GOL · Glycerol · additive · 2 copies · chains A, B

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

Pockets

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

Interfaces

1 interface between chains.

• A–B · 1981 Ų buried · 39 hydrogen bonds · protein-protein

Compared structures

• 5JMP · Structure of Plasmodium falciparum DXR in complex with a beta-substituted fosmidomycin… · the same entry in another collection · chain A against A, TM-score 1.00
• Q8IKG4 · 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 Q8IKG4
• Elsewhere: RCSB PDB 5JMP · PDBe 5JMP · UniProt Q8IKG4