› 2yc5

X-ray diffraction
1.6Å resolution

Inhibitors of the herbicidal target IspD

Released:
DOI: 10.2210/pdb2yc5/pdb
PDB entry 2yc5 coloured by chain, front view.
PDB entry 2yc5 coloured by chain, side view.
PDB entry 2yc5 coloured by chain, top view.
Source organism: Arabidopsis thaliana
Primary publication:
Inhibitors of the herbicidal target IspD: allosteric site binding.
Witschel MC, Höffken HW, Seet M, Parra L, Mietzner T, Thater F, Niggeweg R, Röhl F, Illarionov B, Rohdich F, Kaiser J, Fischer M, Bacher A, Diederich F
Angew Chem Int Ed Engl 50 7931-5 (2011)
PMID: 21766403

Function and Biology Details

Reaction catalysed: 
CTP + 2-C-methyl-D-erythritol 4-phosphate = diphosphate + 4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol
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-159673 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase, chloroplastic Chain: A
Molecule details ›
Chain: A
Length: 228 amino acids
Theoretical weight: 25.43 KDa
Source organism: Arabidopsis thaliana
Expression system: Escherichia coli
UniProt:
  • Canonical: P69834 (Residues: 76-302; Coverage: 75%)
Gene names: At2g02500, ISPD, MCT, MECT, MEPCT, T8K22.20
Sequence domains: 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase
Structure domains: Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A

Ligands and Environments

7 bound ligands:
Ligand 6BC 1 x 6BC
Ligand CU 3 x CU
Ligand MG 1 x MG
Ligand CD 3 x CD
Ligand ACT 2 x ACT
Ligand NA 1 x NA
Ligand ZN 1 x ZN
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SLS BEAMLINE X06DA
Spacegroup: R32
Unit cell:
a: 74.9Å b: 74.9Å c: 220.06Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.152 0.15 0.189
Expression system: Escherichia coli

Quick links

Citations

8 review citations

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