› 2gzl

X-ray diffraction
2.5Å resolution

Structure of 2C-methyl-D-erythritol 2,4-clycodiphosphate synthase complexed with a CDP derived fluorescent inhibitor

Released:
DOI: 10.2210/pdb2gzl/pdb
PDB entry 2gzl coloured by chain, front view.
PDB entry 2gzl coloured by chain, side view.
PDB entry 2gzl coloured by chain, top view.
Source organism: Escherichia coli
Primary publication:
Fluorescent inhibitors for IspF, an enzyme in the non-mevalonate pathway for isoprenoid biosynthesis and a potential target for antimalarial therapy.
Crane CM, Kaiser J, Ramsden NL, Lauw S, Rohdich F, Eisenreich W, Hunter WN, Bacher A, Diederich F
Angew Chem Int Ed Engl 45 1069-74 (2006)
PMID: 16392111

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 domain:

Structure analysis Details

Assembly composition:
homo trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-158656 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase Chain: A
Molecule details ›
Chain: A
Length: 159 amino acids
Theoretical weight: 16.93 KDa
Source organism: Escherichia coli
Expression system: Escherichia coli BL21
UniProt:
  • Canonical: P62617 (Residues: 1-157; Coverage: 99%)
Gene names: JW2716, b2746, ispF, mecS, ygbB
Sequence domains: YgbB family
Structure domains: 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase

Ligands and Environments

3 bound ligands:
Ligand ZN 1 x ZN
Ligand 2AA 1 x 2AA
Ligand GPP 1 x GPP
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID29
Spacegroup: I213
Unit cell:
a: 145.098Å b: 145.098Å c: 145.098Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.209 0.207 0.235
Expression system: Escherichia coli BL21

Quick links

Citations

5 review citations

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

2 mentions without citation

New Insight into Isoprenoids Biosynthesis Process and Future Prospects for Drug Designing in Plasmodium.
Saggu et al. (2016)
1 more