Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A 

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

Macromolecule Content

• Total Structure Weight: 64753.43 
• Atom Count: 4754 
• Residue Count: 544 
• Unique protein chains: 1

5U3V

Human PPARdelta ligand-binding domain in complexed with specific agonist 6

• DOI: 10.2210/pdb5U3V/pdb

• Classification: protein binding/activator
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)


• Deposited: 2016-12-03 Released: 2017-03-22 
• Deposition Author(s): Wu, C.-C., Baiga, T.J., Downes, M., La Clair, J.J., Atkins, A.R., Richard, S.B., Stockley-Noel, T.A., Bowman, M.E., Evans, R.M., Noel, J.P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.84 Å
• R-Value Free: 0.244 
• R-Value Work: 0.200 

Literature

Structural basis for specific ligation of the peroxisome proliferator-activated receptor delta.

Wu, C.C., Baiga, T.J., Downes, M., La Clair, J.J., Atkins, A.R., Richard, S.B., Fan, W., Stockley-Noel, T.A., Bowman, M.E., Noel, J.P., Evans, R.M.

(2017) Proc. Natl. Acad. Sci. U.S.A. 114: E2563-E2570

• PubMed: 28320959 
• DOI: 10.1073/pnas.1621513114
• Primary Citation of Related Structures:  
  5U46, 5U45, 5U44, 5U43, 5U42, 5U41, 5U40, 5U3Z, 5U3Y, 5U3X, 5U3W, 5U3U, 5U3T, 5U3S, 5U3R, 5U3Q


• PubMed Abstract: 
  

The peroxisome proliferator-activated receptor (PPAR) family comprises three subtypes: PPARα, PPARγ, and PPARδ. PPARδ transcriptionally modulates lipid metabolism and the control of energy homeostasis; therefore, PPARδ agonists are promising agents for treating a variety of metabolic disorders. In the present study, we develop a panel of rationally designed PPARδ agonists. The modular motif affords efficient syntheses using building blocks optimized for interactions with subtype-specific residues in the PPARδ ligand-binding domain (LBD). A combination of atomic-resolution protein X-ray crystallographic structures, ligand-dependent LBD stabilization assays, and cell-based transactivation measurements delineate structure-activity relationships (SARs) for PPARδ-selective targeting and structural modulation. We identify key ligand-induced conformational transitions of a conserved tryptophan side chain in the LBD that trigger reorganization of the H2'-H3 surface segment of PPARδ. The subtype-specific conservation of H2'-H3 sequences suggests that this architectural remodeling constitutes a previously unrecognized conformational switch accompanying ligand-dependent PPARδ transcriptional regulation.

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Organizational Affiliation: 

Howard Hughes Medical Institute, The Salk Institute for Biological Studies, La Jolla, CA 92037.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Peroxisome proliferator-activated receptor delta	A, B	272	Homo sapiens	Mutation(s): 0  Gene Names: PPARD (NR1C2, PPARB)
Find proteins for Q03181 (Homo sapiens) Go to Gene View: PPARD Go to UniProtKB:  Q03181

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
B7G	A	HEPTYL-BETA-D-GLUCOPYRANOSIDE C13 H26 O6 NIDYWHLDTIVRJT-UJPOAAIJSA-N
7TY	A, B	6-[2-({cyclopentyl[4-(furan-3-yl)benzene-1-carbonyl]amino}methyl)phenoxy]hexanoic acid C29 H33 N O5 NAVKABWFOLEGSI-UHFFFAOYSA-N
PEG	A, B	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
PGO	A, B	S-1,2-PROPANEDIOL C3 H8 O2 DNIAPMSPPWPWGF-VKHMYHEASA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CME	A, B	L-PEPTIDE LINKING	C5 H11 N O3 S2		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.84 Å
• R-Value Free: 0.244 
• R-Value Work: 0.200 
• Space Group: P 1 2₁ 1

Unit Cell:

Length (Å)	Angle (°)
a = 39.610	α = 90.00
b = 95.050	β = 97.87
c = 96.320	γ = 90.00

Software Package:

Software Name	Purpose
PHASER	phasing
HKL-2000	data reduction
PHENIX	refinement
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2016-12-03 
• Released Date: 2017-03-22 
• Deposition Author(s): Wu, C.-C., Baiga, T.J., Downes, M., La Clair, J.J., Atkins, A.R., Richard, S.B., Stockley-Noel, T.A., Bowman, M.E., Evans, R.M., Noel, J.P.

Revision History 

• Version 1.0: 2017-03-22
  Type: Initial release
• Version 1.1: 2017-03-29
  Type: Database references
• Version 1.2: 2017-04-05
  Type: Database references