2XD9 | pdb_00002xd9

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

• PDB DOI: https://doi.org/10.2210/pdb2XD9/pdb

• Classification: LYASE
• Organism(s): Helicobacter pylori
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2010-04-30 Released: 2010-11-24 
• Deposition Author(s): Paz, S., Tizon, L., Otero, J.M., Llamas-Saiz, A.L., Fox, G.C., van Raaij, M.J., Lamb, H., Hawkins, A.R., Lapthorn, A.J., Castedo, L., Gonzalez-Bello, C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 
  0.250 (Depositor), 0.259 (DCC) 
• R-Value Work: 
  0.210 (Depositor), 0.213 (DCC) 
• R-Value Observed: 
  0.212 (Depositor) 

Starting Model: experimental

Literature

Tetrahydrobenzothiophene derivatives: conformationally restricted inhibitors of type II dehydroquinase.

Paz, S., Tizon, L., Otero, J.M., Llamas-Saiz, A.L., Fox, G.C., van Raaij, M.J., Lamb, H., Hawkins, A.R., Lapthorn, A.J., Castedo, L., Gonzalez-Bello, C.

(2011) ChemMedChem 6: 266-272

• PubMed: 21275050 
• DOI: https://doi.org/10.1002/cmdc.201000343
• Primary Citation Related Structures: 
  2XD9, 2XDA

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Organizational Affiliation: 
• Departamento de Química Orgánica y Centro Singular de Investigación en Química Biológica y Materiales Moleculares, Universidad de Santiago de Compostela calle Jenaro de la Fuente s/n, 15782 Santiago de Compostela, Spain.

Biological Assembly 1  

Global Symmetry: Tetrahedral - T  (Explore in 3D)
Global Stoichiometry: Homo 12-mer - A12 

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

Macromolecule Content 

• Total Structure Weight: 56.31 kDa 
• Atom Count: 3,944 
• Modeled Residue Count: 457 
• Deposited Residue Count: 501 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3-DEHYDROQUINATE DEHYDRATASE	A, B, C	167	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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
XD9	D [auth A], E [auth B], F [auth C]	(4R,6R,7S)-4,6,7-TRIHYDROXY-2-[(1E)-PROP-1-EN-1-YL]-4,5,6,7-TETRAHYDRO-1-BENZOTHIOPHENE-4-CARBOXYLIC ACID C12 H14 O5 S XBFFFFBWIVSOII-PJMUFDJCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free:  0.250 (Depositor), 0.259 (DCC) 
• R-Value Work:  0.210 (Depositor), 0.213 (DCC) 
• R-Value Observed: 0.212 (Depositor) 

Space Group: P 4₂ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 100.217	α = 90
b = 100.217	β = 90
c = 103.934	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-11-24 
Deposition Author(s): Paz, S., Tizon, L., Otero, J.M., Llamas-Saiz, A.L., Fox, G.C., van Raaij, M.J., Lamb, H., Hawkins, A.R., Lapthorn, A.J., Castedo, L., Gonzalez-Bello, C.

Revision History  

• Version 1.0: 2010-11-24
  Type: Initial release
  
• Version 1.1: 2011-12-21
  Changes: Database references, Version format compliance
• Version 1.2: 2012-10-31
  Changes: Database references
• Version 1.3: 2018-02-07
  Changes: Database references, Structure summary
• Version 1.4: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description