8HHP

Crystal structure of PPARg-LBD complexed with three partial agonists, one nTZDpa and two LT175

• PDB DOI: https://doi.org/10.2210/pdb8HHP/pdb

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


• Deposited: 2022-11-16 Released: 2023-11-22 
• Deposition Author(s): Kojima, H., Itoh, T.
• Funding Organization(s): Japan Agency for Medical Research and Development (AMED)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.45 Å
• R-Value Free: 0.286 
• R-Value Work: 0.214 
• R-Value Observed: 0.221 

Literature

Covalent Modifier Discovery by Hydrogen/Deuterium Exchange Mass Spectrometry (HDX-MS)

Kojima, H., Yanagi, R., Higuchi, E., Yoshizawa, M., Shimodaira, T., Kumagai, M., Egawa, D., Ohashi, N., Ishida, H., Yamamoto, K., Itoh, T.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 32.51 kDa 
• Atom Count: 2,209 
• Modelled Residue Count: 263 
• Deposited Residue Count: 276 
• Unique protein chains: 1

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
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
NZA	B [auth A]	5-CHLORO-1-(4-CHLOROBENZYL)-3-(PHENYLTHIO)-1H-INDOLE-2-CARBOXYLIC ACID C22 H15 Cl2 N O2 S VUPOTURDKDMIGQ-UHFFFAOYSA-N
LRG (Subject of Investigation/LOI)	C [auth A], D [auth A]	(2S)-2-(biphenyl-4-yloxy)-3-phenylpropanoic acid C21 H18 O3 TZTPJJNNACUQQR-FQEVSTJZSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.45 Å
• R-Value Free: 0.286 
• R-Value Work: 0.214 
• R-Value Observed: 0.221 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.5	α = 90
b = 60.5	β = 90
c = 162.26	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-11-22 
Deposition Author(s): Kojima, H., Itoh, T.

---

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

Revision History  

• Version 1.0: 2023-11-22
  Type: Initial release