8DKN: PPARg

PPARg bound to T0070907 and Co-R peptide. Determined by X-ray diffraction at 1.95 Å resolution. Released 7 Sept 2022.

Method: X-ray diffraction
Resolution: 1.95 Å
Organism: Homo sapiens
Chains: 2
Atoms: 2,304
Mol. weight: 33.46 kDa
Ligands: EEY, CXS
Released: 7 Sept 2022

Explore 8DKN in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8DKN contains 16 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: 15 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	235-253	19
α-helix	258-266	9
α-helix	272-274	3
β-strand	275-277	3	1
α-helix	280-284	5
α-helix	302-304	3
α-helix	305-316	12
α-helix	318-329	12
α-helix	339-361	23
β-strand	362-363	2	1
β-strand	366-369	4	1
β-strand	374-377	4	1
α-helix	378-383	6
α-helix	388-390	3
α-helix	393-404	12
α-helix	409-420	12
α-helix	433-452	20
α-helix	459-485	27
α-helix	495-501	7

Chain C: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	5-13	9

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Peroxisome proliferator-activated receptor gamma	A	protein	273	Homo sapiens	P37231 (AlphaFold model)
Nuclear receptor corepressor 1 peptide	C	protein	13	Homo sapiens	O75376 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>8DKN_1 Peroxisome proliferator-activated receptor gamma (chains A)
GPESADLRALAKHLYDSYIKSFPLTKAKARAILTGKTTDKSPFVIYDMNSLMMGEDKIKF
KHITPLQEQSKEVAIRIFQGCQFRSVEAVQEITEYAKSIPGFVNLDLNDQVTLLKYGVHE
IIYTMLASLMNKDGVLISEGQGFMTREFLKSLRKPFGDFMEPKFEFAVKFNALELDDSDL
AIFIAVIILSGDRPGLLNVKPIEDIQDNLLQALELQLKLNHPESSQLFAKLLQKMTDLRQ
IVTEHVQLLQVIKKTETDMSLHPLLQEIYKDLY

Sequence of entity 2 (C), FASTA

>8DKN_2 Nuclear receptor corepressor 1 peptide (chains C)
NLGLEDIIRKALM

Ligands and cofactors

ID	Name	Formula	Copies
EEY	2-chloro-5-nitro-N-(pyridin-4-yl)benzamide	C12 H8 Cl N3 O3	1
CXS	3-cyclohexyl-1-propylsulfonic acid	C9 H19 N O3 S	2

Water and common crystallization additives (SO4) are not listed.

Primary citation

Biochemical and structural basis for the pharmacological inhibition of nuclear hormone receptor PPAR gamma by inverse agonists. Irwin, S., Karr, C., Furman, C. et al. J Biol Chem (2022) 298:102539-102539. DOI 10.1016/j.jbc.2022.102539 · PubMed

Other PDB entries of the same protein (UniProt P37231 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9F7W 1.25 Å, Human PPARgamma ligand binding domain in complex with co-activator 1alpha peptide and…
8BF1 1.36 Å, High-resolution structure of unliganded PPAR gamma in complex with the peptide PGC-1 alpha
9V8G 1.39 Å, PPARgamma ligand-binding domain in complex with PG08-NL
9V8H 1.39 Å, PPARgamma ligand-binding domain in complex with PG08-NL and rosiglitazone
8FKC 1.42 Å, Crystal structure of PPARgamma ligand-binding domain in complex with N-CoR peptide and…
6MS7 1.43 Å, Peroxisome proliferator-activated receptor gamma ligand binding domain in complex with a…
9V8D 1.44 Å, PPARgamma ligand-binding domain in complex with PG08
3U9Q 1.52 Å, Ligand binding domain of PPARgamma complexed with Decanoic Acid and PGC-1a peptide
8B94 1.55 Å, Crystal structure of PPARG and NCOR2 with BAY-5516, an inverse agonist
8DKV 1.59 Å, PPARg bound to JTP-426467 and Co-R peptide
3B1M 1.6 Å, Crystal structure of the PPARgamma-LBD complexed with a cercosporamide derivative…
3V9V 1.6 Å, Crystal structure of the PPARgamma-LBD complexed with a cercosporamide derivative…

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