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: 2.40 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.192 

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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: https://doi.org/10.1111/j.1745-7254.2008.00808.x
  • Primary Citation of Related Structures:  
    3B7J

  • 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], 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: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
(3R)-hydroxymyristoyl-acyl carrier protein dehydratase
A, B, C, D, E
A, B, C, D, E, F
159Helicobacter pyloriMutation(s): 0 
Gene Names: fabZ
EC: 4.2.1
UniProt
Find proteins for Q5G940 (Helicobacter pylori)
Explore Q5G940 
Go to UniProtKB:  Q5G940
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5G940
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
JUG
Query on JUG
Download Ideal Coordinates CCD File 
L [auth B],
O [auth C]		5-hydroxynaphthalene-1,4-dione
C10 H6 O3
KQPYUDDGWXQXHS-UHFFFAOYSA-N
BEN
Query on BEN
Download Ideal Coordinates CCD File 
H [auth A]
J [auth B]
K [auth B]
N [auth C]
R [auth E]
H [auth A],
J [auth B],
K [auth B],
N [auth C],
R [auth E],
S [auth E],
U [auth F]
BENZAMIDINE
C7 H8 N2
PXXJHWLDUBFPOL-UHFFFAOYSA-N
CL
Query on CL
Download Ideal Coordinates CCD File 
G [auth A]
I [auth B]
M [auth C]
P [auth D]
Q [auth E]
G [auth A],
I [auth B],
M [auth C],
P [auth D],
Q [auth E],
T [auth F]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Binding Affinity Annotations 
IDSourceBinding Affinity
JUG PDBBind:  3B7J Ki: 6800 (nM) from 1 assay(s)
Binding MOAD:  3B7J Ki: 6800 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 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
b = 100.369β = 90
c = 186.236γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
CNSrefinement
PDB_EXTRACTdata extraction
CrystalCleardata collection
CNSphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-09-02
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2023-11-01
    Changes: Data collection, Database references, Derived calculations, Refinement description