5Y2T: Peroxisome proliferator-activated receptor gamma

Structure of PPARgamma ligand binding domain - lobeglitazone complex. Determined by X-ray diffraction at 1.7 Å resolution. Released 20 Dec 2017.

Method: X-ray diffraction
Resolution: 1.7 Å
Organism: Homo sapiens
Chains: 2
Atoms: 4,704
Mol. weight: 67.71 kDa
Ligands: 8LX
Released: 20 Dec 2017

Explore 5Y2T in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5Y2T contains 31 α-helices and 8 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	208-225	18
α-helix	230-238	9
α-helix	244-246	3
β-strand	247-249	3	1
α-helix	252-261	10
α-helix	277-302	26
α-helix	306-308	3
α-helix	311-332	22
β-strand	334-335	2	1
β-strand	338-341	4	1
α-helix	342-344	3
β-strand	346-349	4	1
α-helix	350-354	5
α-helix	357	1
α-helix	365-375	11
α-helix	381-392	12
α-helix	403-424	22
α-helix	431-459	29
α-helix	467-473	7

Chain B: 16 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	206-225	20
α-helix	230-237	8
α-helix	246	1
β-strand	247-249	3	2
α-helix	252-261	10
α-helix	277-301	25
α-helix	306-308	3
α-helix	311-332	22
β-strand	334-335	2	2
β-strand	338-341	4	2
α-helix	342-344	3
β-strand	346-349	4	2
α-helix	350-354	5
α-helix	357	1
α-helix	360-362	3
α-helix	365-375	11
α-helix	381-392	12
α-helix	403-424	22
α-helix	431-457	27
α-helix	467-472	6

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Peroxisome proliferator-activated receptor gamma	A, B	protein	294	Homo sapiens	P37231 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>5Y2T_1 Peroxisome proliferator-activated receptor gamma (chains A, B)
MGSSHHHHHHSSGLVPRGSAMGSESADLRALAKHLYDSYIKSFPLTKAKARAILTGKTTD
KSPFVIYDMNSLMMGEDKIKFKHITPLQEQSKEVAIRIFQGCQFRSVEAVQEITEYAKSI
PGFVNLDLNDQVTLLKYGVHEIIYTMLASLMNKDGVLISEGQGFMTREFLKSLRKPFGDF
MEPKFEFAVKFNALELDDSDLAIFIAVIILSGDRPGLLNVKPIEDIQDNLLQALELQLKL
NHPESSQLFAKLLQKMTDLRQIVTEHVQLLQVIKKTETDMSLHPLLQEIYKDLY

Ligands and cofactors

ID	Name	Formula	Copies
8LX	(5S)-5-[[4-[2-[[6-(4-methoxyphenoxy)pyrimidin-4-yl]-methyl-amino]ethoxy]phenyl]…	C24 H24 N4 O5 S	2

Primary citation

Structures of PPAR gamma complexed with lobeglitazone and pioglitazone reveal key determinants for the recognition of antidiabetic drugs. Lee, M.A., Tan, L., Yang, H. et al. Sci Rep (2017) 7:16837-16837. DOI 10.1038/s41598-017-17082-x · 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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