3CWD

Molecular recognition of nitro-fatty acids by PPAR gamma

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.233 
  • R-Value Observed: 0.236 

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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: https://doi.org/10.1038/nsmb.1447
  • Primary Citation of Related Structures:  
    3CWD

  • 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 binding domain bound to nitrated linoleic acid, a potent endogenous ligand of PPAR gamma ...

    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
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Peroxisome proliferator-activated receptor gamma
A, B
270Homo sapiensMutation(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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP37231
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
SRC1-2 PEPTIDE
C, D
16N/AMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q15788 (Homo sapiens)
Explore Q15788 
Go to UniProtKB:  Q15788
PHAROS:  Q15788
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ15788
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
LNB
Query on LNB
Download Ideal Coordinates CCD File 
F [auth A],
H [auth B]		(9Z,12E)-12-nitrooctadeca-9,12-dienoic acid
C18 H31 N O4
ZYFTUIURWQWFKQ-QIAGQCQHSA-N		 Ligand Interaction
LNA
Query on LNA
Download Ideal Coordinates CCD File 
E [auth A],
G [auth B]		(9E,12Z)-10-nitrooctadeca-9,12-dienoic acid
C18 H31 N O4
LELVHAQTWXTCLY-XYWKCAQWSA-N		 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
LNB BindingDB:  3CWD IC50: 410 (nM) from 1 assay(s)
EC50: min: 45, max: 70 (nM) from 2 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.233 
  • R-Value Observed: 0.236 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 84.043α = 90
b = 86.197β = 90
c = 97.35γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

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