3CWD | pdb_00003cwd

Molecular recognition of nitro-fatty acids by PPAR gamma

• PDB DOI: https://doi.org/10.2210/pdb3CWD/pdb

• Classification: TRANSCRIPTION
• Organism(s): Homo sapiens
• Mutation(s): No 


• Deposited: 2008-04-21 Released: 2008-07-08 
• Deposition Author(s): Martynowski, D., Li, Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.290 (Depositor), 0.302 (DCC) 
• R-Value Work: 
  0.233 (Depositor), 0.248 (DCC) 
• R-Value Observed: 
  0.236 (Depositor) 

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

• PubMed: 18604218 
• DOI: https://doi.org/10.1038/nsmb.1447
• Primary Citation 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. Structural and functional studies of receptor-ligand interactions reveal the molecular basis of PPAR gamma discrimination of various naturally occurring fatty acid derivatives.

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Organizational Affiliation: 
• Department of Pharmaceutical Sciences, Center for Pharmacogenetics, 709 Salk Hall, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, USA. [e-mail]

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 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 66.85 kDa 
• Atom Count: 4,798 
• Modeled Residue Count: 549 
• Deposited Residue Count: 572 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peroxisome proliferator-activated receptor gamma	A, B	270	Homo sapiens	Mutation(s): 0
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
SRC1-2 PEPTIDE	C, D	16	Homo sapiens	Mutation(s): 0  Gene Names: NCOA1 EC: 2.3.1.48
UniProt & NIH Common Fund Data Resources
Find proteins for Q15788 (Homo sapiens) Explore Q15788  Go to UniProtKB:  Q15788
PHAROS:  Q15788 GTEx:  ENSG00000084676

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
LNB	F [auth A], H [auth B]	(9Z,12E)-12-nitrooctadeca-9,12-dienoic acid C18 H31 N O4 ZYFTUIURWQWFKQ-QIAGQCQHSA-N
LNA	E [auth A], G [auth B]	(9E,12Z)-10-nitrooctadeca-9,12-dienoic acid C18 H31 N O4 LELVHAQTWXTCLY-XYWKCAQWSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.290 (Depositor), 0.302 (DCC) 
• R-Value Work:  0.233 (Depositor), 0.248 (DCC) 
• R-Value Observed: 0.236 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.043	α = 90
b = 86.197	β = 90
c = 97.35	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-07-08 
Deposition Author(s): Martynowski, D., Li, Y.

Revision History  

• Version 1.0: 2008-07-08
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2024-02-21
  Changes: Data collection, Database references, Derived calculations