3X1I

hPPARgamma Ligand binding domain in complex with 6-oxo-tetracosahexaenoic acid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.229 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Characterization of Covalent Bond Formation between PPAR gamma and Oxo-Fatty Acids

Egawa, D.Itoh, T.Yamamoto, K.

(2015) Bioconjug.Chem. --: --

  • DOI: 10.1021/acs.bioconjchem.5b00021
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Covalent modification of proteins is important for normal cellular regulation. Here, we report on the covalent modification of peroxisome proliferator-activated receptor γ (PPARγ), an important drug target, by oxo-fatty acids. In this study, ESI mass ...

    Covalent modification of proteins is important for normal cellular regulation. Here, we report on the covalent modification of peroxisome proliferator-activated receptor γ (PPARγ), an important drug target, by oxo-fatty acids. In this study, ESI mass spectroscopy showed that the reactivities of oxo-fatty acids with PPARγ are different from one another and that these behaviors are related to the structure of the fatty acids. X-ray crystallography showed that three oxo-fatty acids all bound to the same residue of PPARγ (Cys285), but displayed different hydrogen bonding modes. Moreover, fatty acids formed covalent bonds with both PPARγ moieties in the homodimer, one in an active conformation and the other in an alternative conformation. These two conformations may explain why covalently bound fatty acids show partial rather than full agonist activity.


    Organizational Affiliation

    Laboratory of Drug Design and Medicinal Chemistry, Showa Pharmaceutical University, 3-3165 Higashi-Tamagawagakuen, Machida, Tokyo 194-8543, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Peroxisome proliferator-activated receptor gamma
A, B
276Homo sapiensMutation(s): 0 
Gene Names: PPARG (NR1C3)
Find proteins for P37231 (Homo sapiens)
Go to Gene View: PPARG
Go to UniProtKB:  P37231
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
66B
Query on 66B

Download SDF File 
Download CCD File 
A, B
(8E,12Z,15Z,18Z,21Z)-6-oxotetracosa-8,12,15,18,21-pentaenoic acid
C24 H36 O3
SOUDNDRWZSIFBW-IIFHDYRKSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.229 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 93.340α = 90.00
b = 61.920β = 102.72
c = 118.820γ = 90.00
Software Package:
Software NamePurpose
SERGUIdata collection
MOSFLMdata reduction
REFMACrefinement
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-04-08
    Type: Initial release
  • Version 1.1: 2017-11-22
    Type: Refinement description