8FKD

Crystal structure of PPARgamma ligand-binding domain in complex with N-CoR peptide and inverse agonist SR33068

• PDB DOI: https://doi.org/10.2210/pdb8FKD/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: 2.22 Å
• R-Value Free: 0.251 
• R-Value Work: 0.217 
• R-Value Observed: 0.218 

Starting Model: experimental

Literature

Crystal structure of PPARgamma ligand-binding domain in complex with N-CoR peptide and SR33068

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: 34.5 kDa 
• Atom Count: 2,384 
• Modelled Residue Count: 282 
• 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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
Y5O (Subject of Investigation/LOI)	C [auth A]	2-chloro-N-(6-cyanopyridin-3-yl)-5-nitrobenzamide C13 H7 Cl N4 O3 GGFOYRUYCGALNH-UHFFFAOYSA-N
EDO	D [auth A], E [auth A], F [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.22 Å
• R-Value Free: 0.251 
• R-Value Work: 0.217 
• R-Value Observed: 0.218 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.125	α = 90
b = 62.125	β = 90
c = 162.209	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