9V8D | pdb_00009v8d

PPARgamma ligand-binding domain in complex with PG08

• PDB DOI: https://doi.org/10.2210/pdb9V8D/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: 1.44 Å
• R-Value Free: 
  0.201 (Depositor), 0.201 (DCC) 
• R-Value Work: 
  0.172 (Depositor), 0.171 (DCC) 

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: 34.4 kDa 
• Atom Count: 2,484 
• Modeled Residue Count: 278 
• Deposited Residue Count: 300 
• 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
PG08	B	25	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PGE	D [auth A]	TRIETHYLENE GLYCOL C6 H14 O4 ZIBGPFATKBEMQZ-UHFFFAOYSA-N
PEG	C [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
EDO	E [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.44 Å
• R-Value Free:  0.201 (Depositor), 0.201 (DCC) 
• R-Value Work:  0.172 (Depositor), 0.171 (DCC) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.62	α = 90
b = 53.46	β = 105.901
c = 66.91	γ = 90

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