› 2xd9

X-ray diffraction
1.95Å resolution

STRUCTURE OF HELICOBACTER PYLORI TYPE II DEHYDROQUINASE IN COMPLEX WITH INHIBITOR COMPOUND (4R,6R,7S)-4,6,7-Trihydroxy-2-((E)-prop-1- enyl)-4,5,6,7-tetrahydrobenzo(b)thiophene-4-carboxylic acid

Released:
DOI: 10.2210/pdb2xd9/pdb
PDB entry 2xd9 coloured by chain, front view.
PDB entry 2xd9 coloured by chain, side view.
PDB entry 2xd9 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 Chains: A, B, C
Molecule details ›
Chains: A, B, C
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 XD9 3 x XD9
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID23-1
Spacegroup: P4222
Unit cell:
a: 100.217Å b: 100.217Å c: 103.934Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.212 0.21 0.25
Expression system: Escherichia coli BL21(DE3)

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Citations

5 citation in other articles

Bioactive compounds of Crocus sativus L. and their semi-synthetic derivatives as promising anti-Helicobacter pylori, anti-malarial and anti-leishmanial agents.
De Monte et al. (2015)
4 more

1 mention without citation

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