6DCU | pdb_00006dcu

Crystal structure of PPAR gamma co-crystallized with nTZDpa

• PDB DOI: https://doi.org/10.2210/pdb6DCU/pdb

• Classification: dna binding protein/agonist
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2018-05-08 Released: 2019-05-15 
• Deposition Author(s): Mou, T.C., Chrisman, I.M., Hughes, T.S., Sprang, S.R.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.95 Å
• R-Value Free: 
  0.303 (Depositor), 0.300 (DCC) 
• R-Value Work: 
  0.264 (Depositor), 0.260 (DCC) 
• R-Value Observed: 
  0.550 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of PPAR gamma in complex with NMP422

Mou, T.C., Chrisman, I.M., Hughes, T.S., Sprang, S.R.

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 Evidence: gel filtration

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: 70.09 kDa 
• Atom Count: 4,045 
• Modeled Residue Count: 501 
• Deposited Residue Count: 602 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peroxisome proliferator-activated receptor gamma	A, B	301	Homo sapiens	Mutation(s): 0  Gene Names: PPARG, NR1C3
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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NZA	C [auth A], D [auth B]	5-CHLORO-1-(4-CHLOROBENZYL)-3-(PHENYLTHIO)-1H-INDOLE-2-CARBOXYLIC ACID C22 H15 Cl2 N O2 S VUPOTURDKDMIGQ-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
NZA	BindingDB:  6DCU	Kd: 29 (nM) from 1 assay(s)
		IC50: 26 (nM) from 1 assay(s)
		EC50: min: 55, max: 57 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.95 Å
• R-Value Free:  0.303 (Depositor), 0.300 (DCC) 
• R-Value Work:  0.264 (Depositor), 0.260 (DCC) 
• R-Value Observed: 0.550 (Depositor) 

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 94.085	α = 90
b = 94.085	β = 90
c = 192.424	γ = 120

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-05-15 
Deposition Author(s): Mou, T.C., Chrisman, I.M., Hughes, T.S., Sprang, S.R.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	P20GM103546
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)	United States	R00DK103116

Revision History  

• Version 1.0: 2019-05-15
  Type: Initial release
  
• Version 1.1: 2019-12-25
  Changes: Author supporting evidence
• Version 1.2: 2023-10-11
  Changes: Data collection, Database references, Refinement description