3B7J

Crystal structure of (3R)-Hydroxyacyl-Acyl Carrier Protein Dehydratase(FabZ) from Helicobacter pylori complexed with juglone


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.192 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Natural product juglone targets three key enzymes from Helicobacter pylori: inhibition assay with crystal structure characterization

Kong, Y.H.Zhang, L.Yang, Z.Y.Han, C.Hu, L.H.Jiang, H.L.Shen, X.

(2008) ACTA PHARMACOL.SIN. 29: 870-876

  • DOI: 10.1111/j.1745-7254.2008.00808.x

  • PubMed Abstract: 
  • To investigate the inhibition features of the natural product juglone (5- hydroxy-1,4-naphthoquinone) against the three key enzymes from Helicobacter pylori (cystathionine gamma-synthase [HpCGS], malonyl-CoA:acyl carrier protein transacylase [HpFabD] ...

    To investigate the inhibition features of the natural product juglone (5- hydroxy-1,4-naphthoquinone) against the three key enzymes from Helicobacter pylori (cystathionine gamma-synthase [HpCGS], malonyl-CoA:acyl carrier protein transacylase [HpFabD], and beta-hydroxyacyl-ACP dehydratase [HpFabZ]).


    Organizational Affiliation

    Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
(3R)-hydroxymyristoyl-acyl carrier protein dehydratase
A, B, C, D, E, F
159Helicobacter pyloriMutation(s): 0 
Gene Names: fabZ
EC: 4.2.1.59
Find proteins for Q5G940 (Helicobacter pylori)
Go to UniProtKB:  Q5G940
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
A, B, C, D, E, F
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
JUG
Query on JUG

Download SDF File 
Download CCD File 
B, C
5-hydroxynaphthalene-1,4-dione
Juglone
C10 H6 O3
KQPYUDDGWXQXHS-UHFFFAOYSA-N
 Ligand Interaction
BEN
Query on BEN

Download SDF File 
Download CCD File 
A, B, C, E, F
BENZAMIDINE
C7 H8 N2
PXXJHWLDUBFPOL-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
JUGKi: 6800 nM BINDINGMOAD
JUGKi: 6800 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.192 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 73.983α = 90.00
b = 100.369β = 90.00
c = 186.236γ = 90.00
Software Package:
Software NamePurpose
CNSphasing
SCALAdata scaling
CrystalCleardata collection
MOSFLMdata reduction
PDB_EXTRACTdata extraction
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-09-02
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance