6KB4: Peroxisome proliferator-activated receptor alpha

X-ray structure of human PPARalpha ligand binding domain-pemafibrate co-crystals obtained by delipidation and cross-seeding. Determined by X-ray diffraction at 1.42 Å resolution. Released 11 Nov 2020.

Method: X-ray diffraction
Resolution: 1.42 Å
Organism: Homo sapiens
Chains: 1
Atoms: 2,369
Mol. weight: 31.44 kDa
Ligands: P7F
Released: 11 Nov 2020

Explore 6KB4 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6KB4 contains 19 α-helices and 4 β-strands across 1 chain. 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: 19 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	262-264	3
α-helix	266-267	2
α-helix	268-291	24
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	341-345	5
α-helix	348	1
α-helix	351-353	3
α-helix	356-367	12
α-helix	372-383	12
α-helix	394-415	22
α-helix	422-450	29
α-helix	458-464	7

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Peroxisome proliferator-activated receptor alpha	A	protein	273	Homo sapiens	Q07869 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>6KB4_1 Peroxisome proliferator-activated receptor alpha (chains A)
GSHMTADLKSLAKRIYEAYLKNFNMNKVKARVILSGKASNNPPFVIHDMETLCMAEKTLV
AKLVANGIQNKEAEVRIFHCCQCTSVETVTELTEFAKAIPGFANLDLNDQVTLLKYGVYE
AIFAMLSSVMNKDGMLVAYGNGFITREFLKSLRKPFCDIMEPKFDFAMKFNALELDDSDI
SLFVAAIICCGDRPGLLNVGHIEKMQEGIVHVLRLHLQSNHPDDIFLFPKLLQKMADLRQ
LVTEHAQLVQIIKKTESDAALHPLLQEIYRDMY

Ligands and cofactors

ID	Name	Formula	Copies
P7F	(2~{R})-2-[3-[[1,3-benzoxazol-2-yl-[3-(4-methoxyphenoxy)propyl]amino]methyl]phe…	C28 H30 N2 O6	1

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

Primary citation

PPAR alpha Ligand-Binding Domain Structures with Endogenous Fatty Acids and Fibrates. Kamata, S., Oyama, T., Saito, K. et al. iScience (2020) 23:101727-101727. DOI 10.1016/j.isci.2020.101727 · 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…
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)…
6KB8 1.47 Å, X-ray structure of human PPARalpha ligand binding domain-GW7647 co-crystals obtained by…

Browse structure collections

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