5AZT | pdb_00005azt

Ternary complex of hPPARalpha ligand binding domain, 17-oxoDHA and a SRC1 peptide

• PDB DOI: https://doi.org/10.2210/pdb5AZT/pdb

• Classification: DNA BINDING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2015-10-23 Released: 2016-07-06 
• Deposition Author(s): Egawa, D., Itoh, T., Yamamoto, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.45 Å
• R-Value Free: 
  0.308 (Depositor), 0.310 (DCC) 
• R-Value Work: 
  0.253 (Depositor), 0.250 (DCC) 
• R-Value Observed: 
  0.255 (Depositor) 

Literature

17-OxoDHA Is a PPAR alpha/gamma Dual Covalent Modifier and Agonist

Egawa, D., Itoh, T., Akiyama, Y., Saito, T., Yamamoto, K.

(2016) ACS Chem Biol 

• PubMed: 27337155 
• DOI: https://doi.org/10.1021/acschembio.6b00338
• Primary Citation of Related Structures:  
  5AZT, 5AZV


• PubMed Abstract: 
  

  17-Hydroxy docosahexaenoic acid (17-HDHA) is an oxidized form of docosahexaenoic acid (DHA) and known as a specialized proresolving mediator. We found that a further oxidized product, 17-oxodocosahexaenoic acid (17-oxoDHA), activates peroxisome proliferator-activated receptors γ (PPARγ) and PPARα in transcriptional assays and thus can be classified as an α/γ dual agonist. ESI mass spectroscopy and X-ray crystallographic analysis showed that 17-oxoDHA binds to PPARγ and PPARα covalently, making 17-oxoDHA the first of a novel class of PPAR agonists, the PPARα/γ dual covalent agonist. Furthermore, the covalent binding sites were identified as Cys285 for PPARγ and Cys275 for PPARα.

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Organizational Affiliation: 

Laboratory of Drug Design and Medicinal Chemistry, Showa Pharmaceutical University , 3-3165 Higashi-Tamagawagakuen, Machida, Tokyo 194-8543, Japan.

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 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: 63.27 kDa 
• Atom Count: 4,136 
• Modelled Residue Count: 523 
• Deposited Residue Count: 553 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peroxisome proliferator-activated receptor alpha	A, B	269	Homo sapiens	Mutation(s): 1  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
15-meric peptide from Nuclear receptor coactivator 1	C	15	Homo sapiens	Mutation(s): 0  EC: 2.3.1.48
UniProt & NIH Common Fund Data Resources
Find proteins for Q15788 (Homo sapiens) Explore Q15788  Go to UniProtKB:  Q15788
PHAROS:  Q15788 GTEx:  ENSG00000084676

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
4M5	D [auth A], E [auth B]	(4~{Z},7~{Z},10~{Z},13~{Z},19~{Z})-17-oxidanylidenedocosa-4,7,10,13,19-pentaenoic acid C22 H32 O3 XXHHYIQPKMKZSU-BBBWWSJWSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.45 Å
• R-Value Free:  0.308 (Depositor), 0.310 (DCC) 
• R-Value Work:  0.253 (Depositor), 0.250 (DCC) 
• R-Value Observed: 0.255 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.46	α = 90
b = 59.46	β = 90
c = 317.94	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-07-06 
Deposition Author(s): Egawa, D., Itoh, T., Yamamoto, K.

Revision History  

• Version 1.0: 2016-07-06
  Type: Initial release
  
• Version 1.1: 2016-07-13
  Changes: Database references
• Version 1.2: 2020-02-26
  Changes: Data collection, Derived calculations
• Version 1.3: 2024-10-30
  Changes: Data collection, Database references, Structure summary