› 3ke1

X-ray diffraction
2.05Å resolution

Crystal structure of 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase from Burkholderia pseudomallei in complex with a fragment-nucleoside fusion D000161829

Released:
DOI: 10.2210/pdb3ke1/pdb
PDB entry 3ke1 coloured by chain, front view.
PDB entry 3ke1 coloured by chain, side view.
PDB entry 3ke1 coloured by chain, top view.
Source organism: Burkholderia pseudomallei
Primary publication:
Cytidine derivatives as IspF inhibitors of Burkolderia pseudomallei.
Zhang Z, Jakkaraju S, Blain J, Gogol K, Zhao L, Hartley RC, Karlsson CA, Staker BL, Edwards TE, Stewart LJ, Myler PJ, Clare M, Begley DW, Horn JR, Hagen TJ
Bioorg Med Chem Lett 23 6860-3 (2013)
PMID: 24157367

Function and Biology Details

Reaction catalysed: 
2-phospho-4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol = 2-C-methyl-D-erythritol 2,4-cyclodiphosphate + CMP
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
homo trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-174665 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase Chains: A, B, C
Molecule details ›
Chains: A, B, C
Length: 183 amino acids
Theoretical weight: 19.49 KDa
Source organism: Burkholderia pseudomallei
Expression system: Escherichia coli
UniProt:
  • Canonical: Q3JRA0 (Residues: 1-162; Coverage: 100%)
Gene names: BURPS1710b_2511, ispF
Sequence domains: YgbB family
Structure domains: 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase

Ligands and Environments

3 bound ligands:
Ligand ZN 3 x ZN
Ligand 829 3 x 829
Ligand K 1 x K
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU FR-E+ SUPERBRIGHT
Spacegroup: C2
Unit cell:
a: 117.083Å b: 66.964Å c: 59.166Å
α: 90° β: 95.42° γ: 90°
R-values:
R R work R free
0.186 0.184 0.221
Expression system: Escherichia coli

Quick links

Citations

1 review citation

Molecular recognition in chemical and biological systems.
Persch et al. (2015)
4 other articles

4 mentions without citation

Combining functional and structural genomics to sample the essential Burkholderia structome.
Baugh et al. (2013)
3 more