9IWN: Peroxisome proliferator-activated receptor alpha

X-ray structure of human PPARalpha ligand binding domain-intrinsic fatty acid (E. coli origin)-PGC1alpha coactivator peptide co-crystals obtained by cross-seeding. Determined by X-ray diffraction at 1.59 Å resolution. Released 7 May 2025.

Method: X-ray diffraction
Resolution: 1.59 Å
Organism: Homo sapiens
Chains: 2
Atoms: 2,340
Mol. weight: 32.86 kDa
Ligands: PLM
Released: 7 May 2025

Explore 9IWN in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9IWN contains 19 α-helices and 4 β-strands across 2 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 18 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	203-217	15
α-helix	222-230	9
α-helix	237-238	2
β-strand	239-241	3	1
α-helix	244-254	11
α-helix	256-259	4
α-helix	268-292	25
α-helix	297-299	3
α-helix	302-321	20
α-helix	322-324	3
β-strand	325-326	2	1
β-strand	329-332	4	1
β-strand	337-340	4	1
α-helix	341-346	6
α-helix	348	1
α-helix	351-353	3
α-helix	356-366	11
α-helix	372-383	12
α-helix	394-415	22
α-helix	422-450	29
α-helix	455-457	3
α-helix	458-464	7

Chain B: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	689-695	7

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Peroxisome proliferator-activated receptor alpha	A	protein	273	Homo sapiens	Q07869 (AlphaFold model)
Peroxisome proliferator-activated receptor gamma coactivator 1-alpha	B	protein	15	Homo sapiens	Q9UBK2 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>9IWN_1 Peroxisome proliferator-activated receptor alpha (chains A)
GSHMTADLKSLAKRIYEAYLKNFNMNKVKARVILSGKASNNPPFVIHDMETLCMAEKTLV
AKLVANGIQNKEAEVRIFHCCQCTSVETVTELTEFAKAIPGFANLDLNDQVTLLKYGVYE
AIFAMLSSVMNKDGMLVAYGNGFITREFLKSLRKPFCDIMEPKFDFAMKFNALELDDSDI
SLFVAAIICCGDRPGLLNVGHIEKMQEGIVHVLRLHLQSNHPDDIFLFPKLLQKMADLRQ
LVTEHAQLVQIIKKTESDAALHPLLQEIYRDMY

Sequence of entity 2 (B), FASTA

>9IWN_2 Peroxisome proliferator-activated receptor gamma coactivator 1-alpha (chains B)
EAEEPSLLKKLLLAP

Ligands and cofactors

ID	Name	Formula	Copies
PLM	Palmitic acid	C16 H32 O2	1

Water and common crystallization additives (GOL) are not listed.

Primary citation

Competitive Ligand-Induced Recruitment of Coactivators to Specific PPAR alpha / delta / gamma Ligand-Binding Domains Revealed by Dual-Emission FRET and X-Ray Diffraction of Cocrystals. Kamata, S., Honda, A., Yashiro, S. et al. Antioxidants (Basel) (2025) 14. DOI 10.3390/antiox14040494 · PubMed

Other PDB entries of the same protein (UniProt Q07869 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6KAX 1.23 Å, X-ray structure of human PPARalpha ligand binding domain-intrinsic fatty acid (E. coli…
6LXA 1.23 Å, X-ray structure of human PPARalpha ligand binding domain-eicosapentaenoic acid (EPA)…
6KB1 1.25 Å, X-ray structure of human PPARalpha ligand binding domain-tetradecylthioacetic acid (TTA)…
6LX6 1.3 Å, X-ray structure of human PPARalpha ligand binding domain-palmitic acid co-crystals…
6KB0 1.35 Å, X-ray structure of human PPARalpha ligand binding domain-5,8,11,14-eicosatetraynoic acid…
9IWM 1.39 Å, X-ray structure of human PPARalpha ligand binding domain-GW7647-TRAP220 coactivator…
6LX9 1.4 Å, X-ray structure of human PPARalpha ligand binding domain-arachidonic acid co-crystals…
6LX7 1.41 Å, X-ray structure of human PPARalpha ligand binding domain-stearic acid co-crystals…
6KB4 1.42 Å, X-ray structure of human PPARalpha ligand binding domain-pemafibrate co-crystals…
6KB6 1.43 Å, X-ray structure of human PPARalpha ligand binding domain-tetradecylthioacetic acid (TTA)…
6KB3 1.45 Å, X-ray structure of human PPARalpha ligand binding domain-GW7647 co-crystals obtained by…
9VZS 1.46 Å, X-ray structure of human PPARalpha ligand binding domain-10-hydroxystearic acid (10-HSA)…

Browse structure collections

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