› 3ern

X-ray diffraction
2.1Å resolution

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

Released:
DOI: 10.2210/pdb3ern/pdb
PDB entry 3ern coloured by chain, front view.
PDB entry 3ern coloured by chain, side view.
PDB entry 3ern 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 Chains: A, B, C, D, E, F
Molecule details ›
Chains: A, B, C, D, E, F
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 4 x ZN
Ligand CAR 5 x CAR
Ligand SO4 2 x SO4
Ligand GPP 2 x GPP
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID29
Spacegroup: P21
Unit cell:
a: 88.856Å b: 54.236Å c: 118.384Å
α: 90° β: 94.99° γ: 90°
R-values:
R R work R free
0.219 0.218 0.237
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)