6T1V | pdb_00006t1v

Structure of PPARg H494Y mutant in complex with GW1929

• PDB DOI: https://doi.org/10.2210/pdb6T1V/pdb

• Classification: TRANSCRIPTION
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2019-10-06 Released: 2021-04-14 
• Deposition Author(s): Rochel, N.
• Funding Organization(s): French National Research Agency

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.21 Å
• R-Value Free: 
  0.196 (Depositor), 0.197 (DCC) 
• R-Value Work: 
  0.166 (Depositor), 0.165 (DCC) 
• R-Value Observed: 
  0.169 (Depositor) 

Starting Model: experimental

Literature

Structure of a PPARg mutant complex

Rochel, N.

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: 33.91 kDa 
• Atom Count: 2,524 
• Modeled Residue Count: 278 
• Deposited Residue Count: 293 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peroxisome proliferator-activated receptor gamma	A	279	Homo sapiens	Mutation(s): 1  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
Peroxisome proliferator-activated receptor gamma coactivator 1-alpha	B [auth C]	14	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UBK2 (Homo sapiens) Explore Q9UBK2  Go to UniProtKB:  Q9UBK2
PHAROS:  Q9UBK2 GTEx:  ENSG00000109819

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDK (Subject of Investigation/LOI)	C [auth A]	(2~{S})-3-[4-[2-[methyl(pyridin-2-yl)amino]ethoxy]phenyl]-2-[[2-(phenylcarbonyl)phenyl]amino]propanoic acid C30 H29 N3 O4 QTQMRBZOBKYXCG-MHZLTWQESA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
EDK	BindingDB:  6T1V	Ki: min: 0.05, max: 104 (nM) from 6 assay(s)
		EC50: min: 1.5, max: 389 (nM) from 16 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.21 Å
• R-Value Free:  0.196 (Depositor), 0.197 (DCC) 
• R-Value Work:  0.166 (Depositor), 0.165 (DCC) 
• R-Value Observed: 0.169 (Depositor) 

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.349	α = 90
b = 120.741	β = 90
c = 149.843	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: 2021-04-14 
Deposition Author(s): Rochel, N.

---

Funding Organization	Location	Grant Number
French National Research Agency	France	--

Revision History  

• Version 1.0: 2021-04-14
  Type: Initial release
  
• Version 2.0: 2023-01-18
  Type: Coordinate replacement
  Reason: Model completeness
  Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Refinement description, Source and taxonomy, Structure summary
• Version 2.1: 2024-02-07
  Changes: Data collection, Refinement description