› 3esj

X-ray diffraction
2.7Å resolution

Crystal structure of 2C-methyl-D-erythritol 2,4-clycodiphosphate synthase complexed with ligand

Released:
DOI: 10.2210/pdb3esj/pdb
PDB entry 3esj coloured by chain, front view.
PDB entry 3esj coloured by chain, side view.
PDB entry 3esj coloured by chain, top view.
Source organism: Escherichia coli K-12
Primary publication:
A structure-based approach to ligand discovery for 2C-methyl-D-erythritol-2,4-cyclodiphosphate synthase: a target for antimicrobial therapy.
Ramsden NL, Buetow L, Dawson A, Kemp LA, Ulaganathan V, Brenk R, Klebe G, Hunter WN
J Med Chem 52 2531-42 (2009)
PMID: 19320487

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-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: 165 amino acids
Theoretical weight: 17.58 KDa
Source organism: Escherichia coli K-12
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P62617 (Residues: 1-159; Coverage: 100%)
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

4 bound ligands:
Ligand ZN 1 x ZN
Ligand CC7 1 x CC7
Ligand MG 1 x MG
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: 144.498Å b: 144.498Å c: 144.498Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.186 0.184 0.218
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

4 review citations

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

1 mention without citation

A structure-based approach to ligand discovery for 2C-methyl-D-erythritol-2,4-cyclodiphosphate synthase: a target for antimicrobial therapy.
Ramsden et al. (2009)