9T5S | pdb_00009t5s

Crystal structure of human PPARalpha in complex with co-activator PGC-1 alpha peptide and bempedoic acid

• PDB DOI: https://doi.org/10.2210/pdb9T5S/pdb

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


• Deposited: 2025-11-05 Released: 2025-12-17 
• Deposition Author(s): Useini, A., Strater, N., Kuenze, G., Heiker, J.T., Sheikh, B.N.
• Funding Organization(s): German Research Foundation (DFG), Helmholtz Association

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.74 Å
• R-Value Free: 
  0.211 (Depositor), 0.209 (DCC) 
• R-Value Work: 
  0.178 (Depositor), 0.178 (DCC) 
• R-Value Observed: 
  0.180 (Depositor) 

Starting Model: experimental

Literature

Bempedoic acid binds and activates PPARalpha independently of ACSVL1

Useini, A.

To be published.

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 Evidence: gel filtration

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: 70.31 kDa 
• Atom Count: 4,960 
• Modeled Residue Count: 564 
• Deposited Residue Count: 618 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peroxisome proliferator-activated receptor alpha	A, C	290	Homo sapiens	Mutation(s): 0  Gene Names: PPARA, NR1C1, PPAR
UniProt & NIH Common Fund Data Resources
Find proteins for Q07869 (Homo sapiens) Explore Q07869  Go to UniProtKB:  Q07869
PHAROS:  Q07869 GTEx:  ENSG00000186951

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Peroxisome proliferator-activated receptor gamma coactivator 1-alpha	B, D	19	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UBK2 (Homo sapiens) Explore Q9UBK2  Go to UniProtKB:  Q9UBK2
PHAROS:  Q9UBK2 GTEx:  ENSG00000109819

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1JTY (Subject of Investigation/LOI)	E [auth A], F [auth C]	Bempedoic acid C19 H36 O5 HYHMLYSLQUKXKP-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.74 Å
• R-Value Free:  0.211 (Depositor), 0.209 (DCC) 
• R-Value Work:  0.178 (Depositor), 0.178 (DCC) 
• R-Value Observed: 0.180 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.253	α = 90
b = 99.748	β = 99.8
c = 61.612	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
STARANISO	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-12-17 
Deposition Author(s): Useini, A., Strater, N., Kuenze, G., Heiker, J.T., Sheikh, B.N.

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Funding Organization	Location	Grant Number
German Research Foundation (DFG)	Germany	457240345
Helmholtz Association	Germany	--
German Research Foundation (DFG)	Germany	209933838

Revision History  

• Version 1.0: 2025-12-17
  Type: Initial release