3GWX | pdb_00003gwx

MOLECULAR RECOGNITION OF FATTY ACIDS BY PEROXISOME PROLIFERATOR-ACTIVATED RECEPTORS

• PDB DOI: https://doi.org/10.2210/pdb3GWX/pdb

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


• Deposited: 1999-04-26 Released: 2000-04-26 
• Deposition Author(s): Xu, H.E., Lambert, M.H., Montana, V.G., Parks, D.J., Blanchard, S.G., Brown, P.J., Sternbach, D.D., Lehmann, J.M., Wisely, G.B., Willson, T.M., Kliewer, S.A., Milburn, M.V.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.301 (Depositor), 0.305 (DCC) 
• R-Value Work: 
  0.242 (Depositor), 0.245 (DCC) 

Literature

Molecular recognition of fatty acids by peroxisome proliferator-activated receptors.

Xu, H.E., Lambert, M.H., Montana, V.G., Parks, D.J., Blanchard, S.G., Brown, P.J., Sternbach, D.D., Lehmann, J.M., Wisely, G.B., Willson, T.M., Kliewer, S.A., Milburn, M.V.

(1999) Mol Cell 3: 397-403

• PubMed: 10198642 
• DOI: https://doi.org/10.1016/s1097-2765(00)80467-0
• Primary Citation Related Structures: 
  1GWX, 2GWX, 3GWX


• PubMed Abstract: 
  

  The peroxisome proliferator-activated receptors (PPARs) are nuclear receptors for fatty acids (FAs) that regulate glucose and lipid homeostasis. We report the crystal structure of the PPAR delta ligand-binding domain (LBD) bound to either the FA eicosapentaenoic acid (EPA) or the synthetic fibrate GW2433. The carboxylic acids of EPA and GW2433 interact directly with the activation function 2 (AF-2) helix. The hydrophobic tail of EPA adopts two distinct conformations within the large hydrophobic cavity. GW2433 occupies essentially the same space as EPA bound in both conformations. These structures provide molecular insight into the propensity for PPARs to interact with a variety of synthetic and natural compounds, including FAs that vary in both chain length and degree of saturation.

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Organizational Affiliation: 
• Glaxo Wellcome Research and Development, Research Triangle Park, North Carolina 27709, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 62.64 kDa 
• Atom Count: 4,505 
• Modeled Residue Count: 542 
• Deposited Residue Count: 542 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN (PEROXISOME PROLIFERATOR ACTIVATED RECEPTOR (PPAR-DELTA))	A, B	271	Homo sapiens	Mutation(s): 0  Gene Names: PPARD
UniProt & NIH Common Fund Data Resources
Find proteins for Q03181 (Homo sapiens) Explore Q03181  Go to UniProtKB:  Q03181
PHAROS:  Q03181 GTEx:  ENSG00000112033

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EPA	C [auth A], D [auth B]	5,8,11,14,17-EICOSAPENTAENOIC ACID C20 H30 O2 JAZBEHYOTPTENJ-JLNKQSITSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
EPA	BindingDB:  3GWX	IC50: 4000 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.301 (Depositor), 0.305 (DCC) 
• R-Value Work:  0.242 (Depositor), 0.245 (DCC) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.379	α = 90
b = 95.543	β = 97.89
c = 96.181	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2000-04-26 
Deposition Author(s): Xu, H.E., Lambert, M.H., Montana, V.G., Parks, D.J., Blanchard, S.G., Brown, P.J., Sternbach, D.D., Lehmann, J.M., Wisely, G.B., Willson, T.M., Kliewer, S.A., Milburn, M.V.

Revision History  

• Version 1.0: 2000-04-26
  Type: Initial release
  
• Version 1.1: 2008-04-26
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-12-27
  Changes: Data collection, Database references, Derived calculations