› 3ras

X-ray diffraction
2.55Å resolution

Crystal structure of 1-deoxy-D-xylulose 5-phosphate reductoisomerase (DXR) complexed with a lipophilic phosphonate inhibitor

Released:
DOI: 10.2210/pdb3ras/pdb
PDB entry 3ras coloured by chain, front view.
PDB entry 3ras coloured by chain, side view.
PDB entry 3ras coloured by chain, top view.
Source organism: Mycobacterium tuberculosis
Primary publication:
Inhibition of 1-deoxy-D-xylulose-5-phosphate reductoisomerase by lipophilic phosphonates: SAR, QSAR, and crystallographic studies.
Deng L, Diao J, Chen P, Pujari V, Yao Y, Cheng G, Crick DC, Prasad BV, Song Y
J Med Chem 54 4721-34 (2011)
PMID: 21561155

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-161879 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
1-deoxy-D-xylulose 5-phosphate reductoisomerase Chains: A, B
Molecule details ›
Chains: A, B
Length: 398 amino acids
Theoretical weight: 41.7 KDa
Source organism: Mycobacterium tuberculosis
Expression system: Escherichia coli
UniProt:
  • Canonical: P9WNS1 (Residues: 2-389; Coverage: 94%)
Gene names: MTCY274.01c, Rv2870c, dxr
Sequence domains:
Structure domains:

Ligands and Environments


Cofactor: Ligand NDP 2 x NDP
4 bound ligands:
Ligand FM5 2 x FM5
Ligand DCV 2 x DCV
Ligand MN 2 x MN
Ligand SO4 1 x SO4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU FR-E+ SUPERBRIGHT
Spacegroup: P21
Unit cell:
a: 67.25Å b: 65.179Å c: 85.408Å
α: 90° β: 101.28° γ: 90°
R-values:
R R work R free
0.208 0.208 0.278
Expression system: Escherichia coli

Quick links

Citations

4 review citations

Co-operation of TLR4 and raft proteins in LPS-induced pro-inflammatory signaling.
Płóciennikowska et al. (2015)
3 more

2 mentions without citation

Inhibition of 1-deoxy-D-xylulose-5-phosphate reductoisomerase by lipophilic phosphonates: SAR, QSAR, and crystallographic studies.
Deng et al. (2011)
1 more