› 3cf8

X-ray diffraction
2.4Å resolution

Crystal structure of (3R)-Hydroxyacyl-Acyl Carrier Protein Dehydratase (FabZ) from Helicobacter pylori in complex with quercetin

Released:
DOI: 10.2210/pdb3cf8/pdb
PDB entry 3cf8 coloured by chain, front view.
PDB entry 3cf8 coloured by chain, side view.
PDB entry 3cf8 coloured by chain, top view.
Source organism: Helicobacter pylori
Primary publication:
Three flavonoids targeting the beta-hydroxyacyl-acyl carrier protein dehydratase from Helicobacter pylori: crystal structure characterization with enzymatic inhibition assay.
Zhang L, Kong Y, Wu D, Zhang H, Wu J, Chen J, Ding J, Hu L, Jiang H, Shen X
Protein Sci 17 1971-8 (2008)
PMID: 18780820

Function and Biology Details

Reaction catalysed: 
A (3R)-3-hydroxyacyl-[acyl-carrier protein] = a trans-2-enoyl-[acyl-carrier protein] + H(2)O
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
homo hexamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-177141 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
3-hydroxyacyl-[acyl-carrier-protein] dehydratase FabZ Chains: A, B, C, D, E, F
Molecule details ›
Chains: A, B, C, D, E, F
Length: 159 amino acids
Theoretical weight: 18.21 KDa
Source organism: Helicobacter pylori
Expression system: Escherichia coli
UniProt:
  • Canonical: Q5G940 (Residues: 1-159; Coverage: 100%)
Gene names: BB395_03990, DD756_07280, DD767_06730, DDP42_00065, fabZ
Sequence domains: FabA-like domain
Structure domains: Hotdog Thioesterase

Ligands and Environments

3 bound ligands:
Ligand CL 6 x CL
Ligand BEN 6 x BEN
Ligand QUE 2 x QUE
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU
Spacegroup: P212121
Unit cell:
a: 73.987Å b: 100.438Å c: 186.009Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.193 0.193 0.226
Expression system: Escherichia coli

Quick links

Citations

27 review citations

Review on plant antimicrobials: a mechanistic viewpoint.
Khameneh et al. (2019)
26 more

5 mentions without citation

The Potential of Systems Biology to Discover Antibacterial Mechanisms of Plant Phenolics.
Rempe et al. (2017)
4 more