› 2xda

X-ray diffraction
1.85Å resolution

STRUCTURE OF HELICOBACTER PYLORI TYPE II DEHYDROQUINASE IN COMPLEX WITH INHIBITOR COMPOUND (4R,6R,7S)-2-(2-Cyclopropyl)ethyl-4,6,7- trihydroxy-4,5,6,7-tetrahydrobenzo(b)thiophene-4-carboxylic acid

Released:
DOI: 10.2210/pdb2xda/pdb
PDB entry 2xda coloured by chain, front view.
PDB entry 2xda coloured by chain, side view.
PDB entry 2xda coloured by chain, top view.
Source organism: Helicobacter pylori
Primary publication:
Tetrahydrobenzothiophene derivatives: conformationally restricted inhibitors of type II dehydroquinase.
Paz S, Tizón L, Otero JM, Llamas-Saiz AL, Fox GC, van Raaij MJ, Lamb H, Hawkins AR, Lapthorn AJ, Castedo L, González-Bello C
ChemMedChem 6 266-72 (2011)
PMID: 21275050

Function and Biology Details

Reaction catalysed: 
3-dehydroquinate = 3-dehydroshikimate + H(2)O
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
homo dodecamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-175340 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
3-dehydroquinate dehydratase Chain: A
Molecule details ›
Chain: A
Length: 167 amino acids
Theoretical weight: 18.5 KDa
Source organism: Helicobacter pylori
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q48255 (Residues: 1-167; Coverage: 100%)
Gene names: HP_1038, aroQ
Sequence domains: Dehydroquinase class II
Structure domains: Dehydroquinase, class II

Ligands and Environments

1 bound ligand:
Ligand JPS 1 x JPS
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID23-1
Spacegroup: P4232
Unit cell:
a: 99.64Å b: 99.64Å c: 99.64Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.182 0.18 0.21
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

6 citation in other articles

Effective Estimation of Ligand-Binding Affinity Using Biased Sampling Method.
Ngo et al. (2019)
5 more

2 mentions without citation

Significant reduction in errors associated with nonbonded contacts in protein crystal structures: automated all-atom refinement with PrimeX.
Bell et al. (2012)
1 more