2XDA | pdb_00002xda

STRUCTURE OF HELICOBACTER PYLORI TYPE II DEHYDROQUINASE IN COMPLEX WITH INHIBITOR COMPOUND (4R,6R,7S)-2-(2-Cyclopropyl)ethyl-4,6,7- trihydroxy-4,5,6,7-tetrahydrobenzo(b)thiophene-4-carboxylic acid

PDB DOI: https://doi.org/10.2210/pdb2XDA/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., Castedo, L., Gonzalez-Bello, C.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free:
0.210 (Depositor), 0.214 (DCC)
R-Value Work:
0.180 (Depositor), 0.185 (DCC)
R-Value Observed:
0.182 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

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

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.

Macromolecule Content

Total Structure Weight: 18.8 kDa
Atom Count: 1,328
Modeled Residue Count: 150
Deposited Residue Count: 167
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3-DEHYDROQUINATE DEHYDRATASE	A	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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q48255
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
JPS Query on JPS Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	(4R,6R,7S)-2-(2-CYCLOPROPYLETHYL)-4,6,7-TRIHYDROXY-4,5,6,7-TETRAHYDRO-1-BENZOTHIOPHENE-4-CARBOXYLIC ACID C₁₄ H₁₈ O₅ S ZGKGERUMGXJOHU-UHIISALHSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free: 0.210 (Depositor), 0.214 (DCC)
R-Value Work: 0.180 (Depositor), 0.185 (DCC)
R-Value Observed: 0.182 (Depositor)

Space Group: P 4₂ 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 99.64	α = 90
b = 99.64	β = 90
c = 99.64	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2010-11-24

Deposition Author(s):

Revision History (Full details and data files)

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
Version 1.4: 2023-12-20
Changes: Data collection, Database references, Derived calculations, Other, Refinement description