2XKW | pdb_00002xkw

LIGAND BINDING DOMAIN OF HUMAN PPAR-GAMMA IN COMPLEX WITH THE AGONIST PIOGLITAZONE

• PDB DOI: https://doi.org/10.2210/pdb2XKW/pdb

• Classification: TRANSCRIPTION
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2010-07-14 Released: 2011-08-10 
• Deposition Author(s): Mueller, J.J., Schupp, M., Unger, T., Kintscher, U., Heinemann, U.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.02 Å
• R-Value Free: 
  0.202 (Depositor) 
• R-Value Work: 
  0.162 (Depositor) 
• R-Value Observed: 
  0.164 (Depositor) 

Starting Model: experimental

Literature

Binding Diversity of Pioglitazone by Peroxisome Proliferator-Activated Receptor-Gamma

Mueller, J.J., Schupp, M., Unger, T., Kintscher, U., Heinemann, U.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 63.95 kDa 
• Atom Count: 4,442 
• Modeled Residue Count: 517 
• Deposited Residue Count: 548 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PEROXISOME PROLIFERATOR-ACTIVATED RECEPTOR GAMMA	A, B	274	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P37231 (Homo sapiens) Explore P37231  Go to UniProtKB:  P37231
PHAROS:  P37231 GTEx:  ENSG00000132170

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
P1B	C [auth A], E [auth B]	(5R)-5-{4-[2-(5-ethylpyridin-2-yl)ethoxy]benzyl}-1,3-thiazolidine-2,4-dione C19 H20 N2 O3 S HYAFETHFCAUJAY-QGZVFWFLSA-N
PE4	D [auth A]	2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL C16 H34 O8 PJWQOENWHPEPKI-UHFFFAOYSA-N
EPE	F [auth B]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C8 H18 N2 O4 S JKMHFZQWWAIEOD-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
P1B	BindingDB:  2XKW	Ki: min: 62, max: 1230 (nM) from 8 assay(s)
		Kd: 871 (nM) from 1 assay(s)
		IC50: min: 720, max: 2.20e+4 (nM) from 4 assay(s)
		EC50: min: 98, max: 1.77e+4 (nM) from 26 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.02 Å
• R-Value Free:  0.202 (Depositor) 
• R-Value Work:  0.162 (Depositor) 
• R-Value Observed: 0.164 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 92.861	α = 90
b = 60.411	β = 103.01
c = 119.849	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-08-10 
Deposition Author(s): Mueller, J.J., Schupp, M., Unger, T., Kintscher, U., Heinemann, U.

Revision History  

• Version 1.0: 2011-08-10
  Type: Initial release
  
• Version 1.1: 2019-03-06
  Changes: Data collection, Experimental preparation, Other
• Version 1.2: 2019-05-08
  Changes: Data collection, Experimental preparation
• Version 1.3: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description