› 5dnl

X-ray diffraction
1.53Å resolution

Crystal structure of IGPD from Pyrococcus furiosus in complex with (S)-C348

Released:
DOI: 10.2210/pdb5dnl/pdb
PDB entry 5dnl coloured by chain, front view.
PDB entry 5dnl coloured by chain, side view.
PDB entry 5dnl coloured by chain, top view.
Source organism: Pyrococcus furiosus
Primary publication:
Mirror-Image Packing Provides a Molecular Basis for the Nanomolar Equipotency of Enantiomers of an Experimental Herbicide.
Bisson C, Britton KL, Sedelnikova SE, Rodgers HF, Eadsforth TC, Viner RC, Hawkes TR, Baker PJ, Rice DW
Angew Chem Int Ed Engl 55 13485-13489 (2016)
PMID: 27717128

Function and Biology Details

Reaction catalysed: 
D-erythro-1-(imidazol-4-yl)glycerol 3-phosphate = 3-(imidazol-4-yl)-2-oxopropyl phosphate + H(2)O
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
homo 24-mer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-157733 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Imidazoleglycerol-phosphate dehydratase Chains: A, B, C
Molecule details ›
Chains: A, B, C
Length: 176 amino acids
Theoretical weight: 19.76 KDa
Source organism: Pyrococcus furiosus
Expression system: Escherichia coli
UniProt:
  • Canonical: P58880 (Residues: 1-176; Coverage: 100%)
Gene names: PF1660, hisB
Sequence domains: Imidazoleglycerol-phosphate dehydratase
Structure domains: Imidazole glycerol phosphate dehydratase; domain 1

Ligands and Environments

2 bound ligands:
Ligand MN 6 x MN
Ligand 5DL 3 x 5DL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I04
Spacegroup: I422
Unit cell:
a: 141.27Å b: 141.27Å c: 137.41Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.136 0.135 0.149
Expression system: Escherichia coli

Quick links

Citations

2 citation in other articles

Elucidating the structural basis for differing enzyme inhibitor potency by cryo-EM.
Rawson et al. (2018)
1 more

3 mentions without citation

An experimental assay of the interactions of amino acids from orthologous sequences shaping a complex fitness landscape.
Pokusaeva et al. (2019)
2 more