6A6P

Crystal Structure of Peroxisome Proliferator-Activated Receptor Delta (PPARd)LBD in Complex with DN003316

• PDB DOI: https://doi.org/10.2210/pdb6A6P/pdb

• Classification: STRUCTURAL PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2018-06-29 Released: 2019-07-10 
• Deposition Author(s): Chin, J.W., Cho, S.J., Song, J.Y., Ha, J.H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.228 
• R-Value Work: 0.194 
• R-Value Observed: 0.195 

Starting Model: experimental

Literature

Crystal Structure of Peroxisome Proliferator-Activated Receptor Delta (PPARd)LBD in Complex with DN003316

Chin, J.W., Cho, S.J., Song, J.Y., Ha, J.H.

To be published.

Biological Assembly 1  

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

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

Biological Assembly Evidence: gel filtration

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: 64.41 kDa 
• Atom Count: 4,702 
• Modelled Residue Count: 533 
• Deposited Residue Count: 540 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peroxisome proliferator-activated receptor delta	A, B	270	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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PE3	E [auth A], H [auth B]	3,6,9,12,15,18,21,24,27,30,33,36,39-TRIDECAOXAHENTETRACONTANE-1,41-DIOL C28 H58 O15 ILLKMACMBHTSHP-UHFFFAOYSA-N
9RF	C [auth A], F [auth B]	{2-methyl-4-[({5-[4-(trifluoromethyl)phenyl]-1,3,4-thiadiazol-2-yl}methyl)sulfanyl]phenoxy}acetic acid C19 H15 F3 N2 O3 S2 NLJZRFBMZSIDNW-UHFFFAOYSA-N
B7G	D [auth A], G [auth B]	heptyl beta-D-glucopyranoside C13 H26 O6 NIDYWHLDTIVRJT-UJPOAAIJSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.228 
• R-Value Work: 0.194 
• R-Value Observed: 0.195 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.605	α = 90
b = 95.749	β = 97.91
c = 96.936	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data collection
HKL-2000	data scaling
PHENIX	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-07-10 
Deposition Author(s): Chin, J.W., Cho, S.J., Song, J.Y., Ha, J.H.

Revision History  

• Version 1.0: 2019-07-10
  Type: Initial release
  
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2023-11-22
  Changes: Data collection, Database references, Refinement description, Structure summary