Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PQS (software)

Macromolecule Content

• Total Structure Weight: 20.06 kDa 
• Atom Count: 1582 
• Modelled Residue Count: 168 
• Deposited Residue Count: 176 
• Unique protein chains: 1

2C4W

Type II Dehydroquinase from H. pylori in complex with AH9095

• PDB DOI: 10.2210/pdb2C4W/pdb

• Classification: LYASE
• Organism(s): Helicobacter pylori
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2005-10-24 Released: 2006-02-22 
• Deposition Author(s): Robinson, D.A., Lapthorn, A.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free: 0.190 
• R-Value Work: 0.152 
• R-Value Observed: 0.156 

Literature

Crystal Structures of Helicobacter Pylori Type II Dehydroquinase Inhibitor Complexes: New Directions for Inhibitor Design.

Robinson, D.A., Stewart, K.A., Price, N.C., Chalk, P.A., Coggins, J.R., Lapthorn, A.J.

(2006) J Med Chem 49: 1282

• PubMed: 16480265 
• DOI: 10.1021/jm0505361
• Primary Citation of Related Structures:  
  2C4V, 2C4W, 2C57


• PubMed Abstract: 
  

The crystal structures of the type II dehydroquinase (DHQase) from Helicobacter pylori in complex with three competitive inhibitors have been determined. The inhibitors are the substrate analogue 2,3-anhydroquinate (FA1), citrate, and an oxoxanthene sulfonamide derivative (AH9095). Despite the very different chemical nature of the inhibitors, in each case the primary point of interaction with the enzyme is via the residues that bind the C1 functionalities of the substrate, 3-dehydroquinate, i.e., N76, H102, I103, and H104. The DHQase/AH9095 complex crystal structure shows that sulfonamides can form a scaffold for nonsubstrate-like inhibitors and identifies a large conserved hydrophobic patch at the entrance to the active site as a locus that can be exploited in the development of new ligands.

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Organizational Affiliation: 

Division of Biochemistry and Molecular Biology, Institute of Biomedical and Life Sciences, University of Glasgow, Glasgow G12 8QQ, Scotland, UK.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3-DEHYDROQUINATE DEHYDRATASE	A	176	Helicobacter pylori	Mutation(s): 0  EC: 4.2.1.10
UniProt
Find proteins for Q48255 (Helicobacter pylori (strain ATCC 700392 / 26695)) Explore Q48255  Go to UniProtKB:  Q48255

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GAJ	B [auth A]	N-TETRAZOL-5-YL 9-OXO-9H-XANTHENE-2 SULPHONAMIDE C14 H9 N5 O4 S HJWYZPGYPZNDTN-UHFFFAOYSA-N
GOL	C [auth A], D [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
IMD	E [auth A], F [auth A]	IMIDAZOLE C3 H5 N2 RAXXELZNTBOGNW-UHFFFAOYSA-O

Binding Affinity Annotations
ID	Source	Binding Affinity
GAJ	Binding MOAD:  2C4W	Ki: 2.00e+4 (nM) from 1 assay(s)
	PDBBind:  2C4W	Ki: 2.00e+4 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free: 0.190 
• R-Value Work: 0.152 
• R-Value Observed: 0.156 
• Space Group: F 2 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 131.37	α = 90
b = 131.37	β = 90
c = 131.37	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
EPMR	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2005-10-24 
• Released Date: 2006-02-22 
Deposition Author(s): Robinson, D.A., Lapthorn, A.J.

Revision History  

• Version 1.0: 2006-02-22
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance