9V8E | pdb_00009v8e

PPARgamma ligand-binding domain in complex with PG11

• PDB DOI: https://doi.org/10.2210/pdb9V8E/pdb

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


• Deposited: 2025-05-29 Released: 2025-11-05 
• Deposition Author(s): Sigal, M., Okada, C., Katoh, T., Suga, H., Sengoku, T.
• Funding Organization(s): Japan Agency for Medical Research and Development (AMED)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.215 (Depositor), 0.218 (DCC) 
• R-Value Work: 
  0.173 (Depositor), 0.184 (DCC) 
• R-Value Observed: 
  0.175 (Depositor) 

Starting Model: experimental

Literature

PPARgamma ligand-binding domain in complex with PG08

Sigal, M., Okada, C., Katoh, T., Suga, H., Sengoku, T.

(2025) J Am Chem Soc 

• DOI: https://doi.org/10.1021/jacs.5c13803

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: surface plasmon resonance

Macromolecule Content 

• Total Structure Weight: 33.64 kDa 
• Atom Count: 2,299 
• Modeled Residue Count: 270 
• Deposited Residue Count: 294 
• Unique protein chains: 2

Macromolecules

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

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
PG11	B	19	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PEG	C [auth B]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
N9P	B	L-PEPTIDE LINKING	C8 H10 N2 O2		ALA

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.215 (Depositor), 0.218 (DCC) 
• R-Value Work:  0.173 (Depositor), 0.184 (DCC) 
• R-Value Observed: 0.175 (Depositor) 

Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 106.43	α = 90
b = 106.43	β = 90
c = 59.61	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-11-05 
Deposition Author(s): Sigal, M., Okada, C., Katoh, T., Suga, H., Sengoku, T.

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Funding Organization	Location	Grant Number
Japan Agency for Medical Research and Development (AMED)	Japan	--

Revision History  

• Version 1.0: 2025-11-05
  Type: Initial release
  
• Version 1.1: 2025-11-12
  Changes: Database references