7QA0

Crystal structure of PqsR (MvfR) ligand-binding domain in complex with compound 1456

PDB DOI: https://doi.org/10.2210/pdb7QA0/pdb

Classification: GENE REGULATION
Organism(s): Pseudomonas aeruginosa PAO1
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2021-11-15 Released: 2022-11-23
Deposition Author(s): Schmelz, S., Blankenfeldt, W.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.67 Å
R-Value Free: 0.281
R-Value Work: 0.236
R-Value Observed: 0.238

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Discovery and Optimization of Thiazole-Based Quorum Sensing Inhibitors as Potent Blockers of Pseudomonas Aeruginosa Pathogenicity

Abdelsamie, A.S., Hamed, M.M., Schutz, C., Rohrig, T., Kany, A.M., Schmelz, S., Blankenfeldt, W., Hirsch, A.K.H., Hartmann, R.W., Empting, M.

(2024) SSRN

DOI: https://doi.org/10.2139/ssrn.4789988

Macromolecule Content

Total Structure Weight: 75.37 kDa
Atom Count: 3,145
Modelled Residue Count: 405
Deposited Residue Count: 664
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Multiple virulence factor regulator MvfR	A, B	332	Pseudomonas aeruginosa PAO1	Mutation(s): 0 Gene Names: mvfR, PA1003
UniProt
Find proteins for Q9I4X0 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)) Explore Q9I4X0 Go to UniProtKB: Q9I4X0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9I4X0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
9ZL (Subject of Investigation/LOI) Query on 9ZL Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth B]	C [auth A], D [auth B]	~{N}-[[2-(3-chloranyl-4-propan-2-yloxy-phenyl)-1,3-thiazol-5-yl]methyl]-2-(trifluoromethyl)pyridin-4-amine C₁₉ H₁₇ Cl F₃ N₃ O S GQVXDNRONWTUJQ-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.67 Å
R-Value Free: 0.281
R-Value Work: 0.236
R-Value Observed: 0.238
Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 109.131	α = 90
b = 119.824	β = 90
c = 114.033	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
autoPROC	data processing
STARANISO	data scaling
PHENIX	phasing
autoPROC	data reduction

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2022-11-23

Deposition Author(s):

Blankenfeldt, W.

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2022-11-23
Type: Initial release
Version 1.1: 2024-01-31
Changes: Data collection, Refinement description
Version 1.2: 2024-06-12
Changes: Database references

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.