3VSP

Human PPAR gamma ligand binding domain in complex with a gamma selective agonist mekt28

• PDB DOI: https://doi.org/10.2210/pdb3VSP/pdb

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


• Deposited: 2012-04-30 Released: 2013-05-01 
• Deposition Author(s): Oyama, T., Waku, T., Ohashi, M., Morikawa, K., Miyachi, H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.274 
• R-Value Work: 0.222 
• R-Value Observed: 0.222 

Starting Model: experimental

Literature

Human PPAR gamma ligand binding domain in complex with a gamma selective agonist mekt28

Oyama, T., Waku, T., Ohashi, M., Morikawa, K., Miyachi, H.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 65.58 kDa 
• Atom Count: 4,264 
• Modelled Residue Count: 524 
• Deposited Residue Count: 572 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peroxisome proliferator-activated receptor gamma	A, B	286	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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EK8	C [auth A]	(2R)-2-benzyl-3-[3-({[4-(piperidin-1-yl)benzoyl]amino}methyl)-4-propoxyphenyl]propanoic acid C32 H38 N2 O4 ISYAJDFASPMBOB-HHHXNRCGSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
EK8	BindingDB:  3VSP	Kd: 2.9 (nM) from 1 assay(s)
		EC50: 53 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.274 
• R-Value Work: 0.222 
• R-Value Observed: 0.222 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 93.409	α = 90
b = 60.871	β = 102.95
c = 118.598	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHENIX	model building
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-05-01 
Deposition Author(s): Oyama, T., Waku, T., Ohashi, M., Morikawa, K., Miyachi, H.

Revision History  

• Version 1.0: 2013-05-01
  Type: Initial release
  
• Version 1.1: 2017-11-22
  Changes: Refinement description
• Version 1.2: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description