5U3W

Human PPARdelta ligand-binding domain in complexed with specific agonist 7

• PDB DOI: https://doi.org/10.2210/pdb5U3W/pdb

• Classification: protein binding/activator
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• 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: 1.80 Å
• R-Value Free: 0.243 
• R-Value Work: 0.192 
• R-Value Observed: 0.193 

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content

• Total Structure Weight: 64.26 kDa 
• Atom Count: 4,777 
• Modelled Residue Count: 529 
• Deposited Residue Count: 544 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peroxisome proliferator-activated receptor delta	A, B	272	Homo sapiens	Mutation(s): 0  Gene Names: PPARD, NR1C2, PPARB
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 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
7U1	D [auth A], J [auth B]	6-(2-{[([1,1'-biphenyl]-4-carbonyl)(cyclopropyl)amino]methyl}phenoxy)hexanoic acid C29 H31 N O4 XWRSFMVWMRKGCC-UHFFFAOYSA-N
B7G	C [auth A], E [auth A]	heptyl beta-D-glucopyranoside C13 H26 O6 NIDYWHLDTIVRJT-UJPOAAIJSA-N
PEG	K [auth B]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
PGO	F [auth A], G [auth A], H [auth A], I [auth A]	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: 1.80 Å
• R-Value Free: 0.243 
• R-Value Work: 0.192 
• R-Value Observed: 0.193 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.56	α = 90
b = 94.81	β = 98.27
c = 96.61	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• 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
  Changes: Database references
• Version 1.2: 2017-04-05
  Changes: Database references
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2023-10-04
  Changes: Data collection, Database references, Refinement description, Structure summary