› 4y6r

X-ray diffraction
1.9Å resolution

Structure of Plasmodium falciparum DXR in complex with a beta-substituted fosmidomycin analogue, RC137, and manganese

Released:
DOI: 10.2210/pdb4y6r/pdb
PDB entry 4y6r coloured by chain, front view.
PDB entry 4y6r coloured by chain, side view.
PDB entry 4y6r coloured by chain, top view.
Source organism: Plasmodium falciparum 3D7
Primary publication:
Synthesis and bioactivity of β-substituted fosmidomycin analogues targeting 1-deoxy-D-xylulose-5-phosphate reductoisomerase.
Chofor R, Sooriyaarachchi S, Risseeuw MD, Bergfors T, Pouyez J, Johny C, Haymond A, Everaert A, Dowd CS, Maes L, Coenye T, Alex A, Couch RD, Jones TA, Wouters J, Mowbray SL, Van Calenbergh S
J Med Chem 58 2988-3001 (2015)
PMID: 25781377

Function and Biology Details

Reaction catalysed: 
2-C-methyl-D-erythritol 4-phosphate + NADP(+) = 1-deoxy-D-xylulose 5-phosphate + NADPH
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-184807 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
1-deoxy-D-xylulose 5-phosphate reductoisomerase, apicoplastic Chains: A, B
Molecule details ›
Chains: A, B
Length: 422 amino acids
Theoretical weight: 48.16 KDa
Source organism: Plasmodium falciparum 3D7
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q8IKG4 (Residues: 75-488; Coverage: 85%)
Gene names: DXR, PF14_0641, PF3D7_1467300
Sequence domains:
Structure domains:

Ligands and Environments

4 bound ligands:
Ligand RF7 2 x RF7
Ligand MN 2 x MN
Ligand CL 1 x CL
Ligand SO4 1 x SO4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID29
Spacegroup: P1
Unit cell:
a: 51.399Å b: 54.852Å c: 85.208Å
α: 89.64° β: 105.4° γ: 107.61°
R-values:
R R work R free
0.189 0.187 0.218
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

4 review citations

Targeting Metalloenzymes for Therapeutic Intervention.
Chen et al. (2019)
3 more

1 mention without citation

Mechanism of Action of N-Acyl and N-Alkoxy Fosmidomycin Analogs: Mono- and Bisubstrate Inhibition of IspC from Plasmodium falciparum, a Causative Agent of Malaria.
Girma et al. (2021)