› 5jnl

X-ray diffraction
1.6Å resolution

Structure of Plasmodium falciparum DXR in complex with a beta-substituted fosmidomycin analogue, LC54 and manganese

Released:
DOI: 10.2210/pdb5jnl/pdb
PDB entry 5jnl coloured by chain, front view.
PDB entry 5jnl coloured by chain, side view.
PDB entry 5jnl coloured by chain, top view.
Source organism: Plasmodium falciparum 3D7
Primary publication:
Targeting an Aromatic Hotspot in Plasmodium falciparum 1-Deoxy-d-xylulose-5-phosphate Reductoisomerase with β-Arylpropyl Analogues of Fosmidomycin.
Sooriyaarachchi S, Chofor R, Risseeuw MD, Bergfors T, Pouyez J, Dowd CS, Maes L, Wouters J, Jones TA, Van Calenbergh S, Mowbray SL
ChemMedChem 11 2024-36 (2016)
PMID: 27487410

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 L54 2 x L54
Ligand MN 2 x MN
Ligand GOL 4 x GOL
Ligand EDO 9 x EDO
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID29
Spacegroup: P1
Unit cell:
a: 51.473Å b: 56.035Å c: 86.041Å
α: 103.1° β: 102.89° γ: 100.9°
R-values:
R R work R free
0.179 0.178 0.199
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

2 review citations

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