8ZFN

Crystal Structure of Human PPARgamma Ligand Binding Domain in Complex with GW9662 and BVT.13

• PDB DOI: https://doi.org/10.2210/pdb8ZFN/pdb

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


• Deposited: 2024-05-08 Released: 2024-08-07 
• Deposition Author(s): Shang, J., 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: 2.54 Å
• R-Value Free: 0.321 
• R-Value Work: 0.247 
• R-Value Observed: 0.250 

Starting Model: experimental

Literature

Unanticipated mechanisms of covalent inhibitor and synthetic ligand cobinding to PPAR gamma.

Shang, J., Kojetin, D.J.

(2024) Elife 

• DOI: https://doi.org/10.7554/eLife.99782.1

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 64.26 kDa 
• Atom Count: 4,274 
• Modelled Residue Count: 517 
• Deposited Residue Count: 550 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peroxisome proliferator-activated receptor gamma	A, B	275	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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PLB (Subject of Investigation/LOI)	D [auth A], F [auth B]	2-[(2,4-DICHLOROBENZOYL)AMINO]-5-(PYRIMIDIN-2-YLOXY)BENZOIC ACID C18 H11 Cl2 N3 O4 VNDRRWBKNSHALL-UHFFFAOYSA-N
GW9 (Subject of Investigation/LOI)	C [auth A], E [auth B]	2-chloro-5-nitro-N-phenylbenzamide C13 H9 Cl N2 O3 DNTSIBUQMRRYIU-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.54 Å
• R-Value Free: 0.321 
• R-Value Work: 0.247 
• R-Value Observed: 0.250 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 92.186	α = 90
b = 61.991	β = 102.38
c = 118.841	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
DIALS	data reduction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-08-07 
Deposition Author(s): Shang, J., 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	R01DK124870

Revision History  

• Version 1.0: 2024-08-07
  Type: Initial release
  
• Version 1.1: 2024-10-16
  Changes: Structure summary