8FKF

Crystal structure of PPARgamma ligand-binding domain in complex with N-CoR peptide and inverse agonist SR36706

• PDB DOI: https://doi.org/10.2210/pdb8FKF/pdb

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


• Deposited: 2022-12-21 Released: 2024-04-17 
• Deposition Author(s): MacTavish, B.S., Kojetin, D.J.
• Funding Organization(s): 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: 1.82 Å
• R-Value Free: 0.216 
• R-Value Work: 0.181 
• R-Value Observed: 0.182 

Starting Model: experimental

Literature

Crystal structure of PPARgamma ligand-binding domain in complex with N-CoR peptide and SR36706

MacTavish, B.S., Kojetin, D.J.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 34.65 kDa 
• Atom Count: 2,477 
• Modelled Residue Count: 277 
• Deposited Residue Count: 299 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peroxisome proliferator-activated receptor gamma	A	276	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

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Nuclear receptor corepressor 1	B [auth D]	23	Homo sapiens	Mutation(s): 0  Gene Names: NCOR1, KIAA1047
UniProt & NIH Common Fund Data Resources
Find proteins for O75376 (Homo sapiens) Explore O75376  Go to UniProtKB:  O75376
PHAROS:  O75376 GTEx:  ENSG00000141027

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
Y5X (Subject of Investigation/LOI)	C [auth A]	2-chloro-N-(5-fluoropyridin-3-yl)-5-nitrobenzamide C12 H7 Cl F N3 O3 YYVSYARVIWSRBD-UHFFFAOYSA-N
GOL	H [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO	D [auth A], E [auth A], F [auth A], G [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.82 Å
• R-Value Free: 0.216 
• R-Value Work: 0.181 
• R-Value Observed: 0.182 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.765	α = 90
b = 61.765	β = 90
c = 161.084	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-04-17 
Deposition Author(s): MacTavish, B.S., Kojetin, D.J.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)	United States	6R01DK124870

Revision History  

• Version 1.0: 2024-04-17
  Type: Initial release
  
• Version 1.1: 2024-10-09
  Changes: Structure summary