› 3zhy

X-ray diffraction
2.3Å resolution

Structure of Mycobacterium tuberculosis DXR in complex with a di- substituted fosmidomycin analogue

Released:
DOI: 10.2210/pdb3zhy/pdb
PDB entry 3zhy coloured by chain, front view.
PDB entry 3zhy coloured by chain, side view.
PDB entry 3zhy coloured by chain, top view.
Source organism: Mycobacterium tuberculosis H37Rv
Primary publication:
DXR inhibition by potent mono- and disubstituted fosmidomycin analogues.
Jansson AM, Więckowska A, Björkelid C, Yahiaoui S, Sooriyaarachchi S, Lindh M, Bergfors T, Dharavath S, Desroses M, Suresh S, Andaloussi M, Nikhil R, Sreevalli S, Srinivasa BR, Larhed M, Jones TA, Karlén A, Mowbray SL
J Med Chem 56 6190-9 (2013)
PMID: 23819803

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: 397 amino acids
Theoretical weight: 41.6 KDa
Source organism: Mycobacterium tuberculosis H37Rv
Expression system: Escherichia coli BL21(DE3)
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
2 bound ligands:
Ligand MN 2 x MN
Ligand FM6 2 x FM6
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID23-1
Spacegroup: P43212
Unit cell:
a: 111.74Å b: 111.74Å c: 136.45Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.204 0.201 0.254
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

4 review citations

Molecular docking as a popular tool in drug design, an in silico travel.
de Ruyck et al. (2016)
3 more

1 mention without citation

Over 40 Years of Fosmidomycin Drug Research: A Comprehensive Review and Future Opportunities.
Knak et al. (2022)