3CWD

Molecular recognition of nitro-fatty acids by PPAR gamma


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.233 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Molecular recognition of nitrated fatty acids by PPAR gamma.

Li, Y.Zhang, J.Schopfer, F.J.Martynowski, D.Garcia-Barrio, M.T.Kovach, A.Suino-Powell, K.Baker, P.R.Freeman, B.A.Chen, Y.E.Xu, H.E.

(2008) Nat.Struct.Mol.Biol. 15: 865-867

  • DOI: 10.1038/nsmb.1447

  • PubMed Abstract: 
  • Peroxisome proliferator activated receptor-gamma (PPAR gamma) regulates metabolic homeostasis and adipocyte differentiation, and it is activated by oxidized and nitrated fatty acids. Here we report the crystal structure of the PPAR gamma ligand bindi ...

    Peroxisome proliferator activated receptor-gamma (PPAR gamma) regulates metabolic homeostasis and adipocyte differentiation, and it is activated by oxidized and nitrated fatty acids. Here we report the crystal structure of the PPAR gamma ligand binding domain bound to nitrated linoleic acid, a potent endogenous ligand of PPAR gamma. Structural and functional studies of receptor-ligand interactions reveal the molecular basis of PPAR gamma discrimination of various naturally occurring fatty acid derivatives.


    Organizational Affiliation

    Department of Pharmaceutical Sciences, Center for Pharmacogenetics, 709 Salk Hall, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, USA. yol21@pitt.edu




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Peroxisome proliferator-activated receptor gamma
A, B
270Homo sapiensMutation(s): 0 
Gene Names: PPARG (NR1C3)
Find proteins for P37231 (Homo sapiens)
Go to Gene View: PPARG
Go to UniProtKB:  P37231
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
SRC1-2 PEPTIDE
C, D
16Homo sapiensMutation(s): 0 
Gene Names: NCOA1 (BHLHE74, SRC1)
EC: 2.3.1.48
Find proteins for Q15788 (Homo sapiens)
Go to Gene View: NCOA1
Go to UniProtKB:  Q15788
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
LNA
Query on LNA

Download SDF File 
Download CCD File 
A, B
(9E,12Z)-10-nitrooctadeca-9,12-dienoic acid
C18 H31 N O4
LELVHAQTWXTCLY-XYWKCAQWSA-N
 Ligand Interaction
LNB
Query on LNB

Download SDF File 
Download CCD File 
A, B
(9Z,12E)-12-nitrooctadeca-9,12-dienoic acid
C18 H31 N O4
ZYFTUIURWQWFKQ-QIAGQCQHSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
LNBIC50: 410 nM (100) BINDINGDB
LNBEC50: 45 - 70 nM (100) BINDINGDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.233 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 84.043α = 90.00
b = 86.197β = 90.00
c = 97.350γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data collection
REFMACrefinement
HKL-2000data reduction
AMoREphasing
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-07-08
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance