6MS7: Peroxisome proliferator-activated receptor gamma

Peroxisome proliferator-activated receptor gamma ligand binding domain in complex with a novel selective PPAR-gamma modulator VSP-77. Determined by X-ray diffraction at 1.43 Å resolution. Released 23 Oct 2019.

Method: X-ray diffraction
Resolution: 1.43 Å
Organisms: Homo sapiens, synthetic construct
Chains: 2
Atoms: 2,511
Mol. weight: 33.03 kDa
Ligands: V77
Released: 23 Oct 2019

Explore 6MS7 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6MS7 contains 15 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: 14 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	205-225	21
α-helix	230-237	8
α-helix	244-246	3
β-strand	247-249	3	1
α-helix	252-262	11
α-helix	277-301	25
α-helix	306-308	3
α-helix	311-332	22
β-strand	334-335	2	1
β-strand	338-341	4	1
β-strand	346-349	4	1
α-helix	350-355	6
α-helix	360-362	3
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: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	143-149	7

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Peroxisome proliferator-activated receptor gamma	A	protein	274	Homo sapiens	P37231 (AlphaFold model)
PGC1 LXXLL motif	B	protein	11	synthetic construct	Q9UBK2 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>6MS7_1 Peroxisome proliferator-activated receptor gamma (chains A)
GSPESADLRALAKHLYDSYIKSFPLTKAKARAILTGKTTDKSPFVIYDMNSLMMGEDKIK
FKHITPLQEQSKEVAIRIFQGCQFRSVEAVQEITEYAKSIPGFVNLDLNDQVTLLKYGVH
EIIYTMLASLMNKDGVLISEGQGFMTREFLKSLRKPFGDFMEPKFEFAVKFNALELDDSD
LAIFIAVIILSGDRPGLLNVKPIEDIQDNLLQALELQLKLNHPESSQLFAKLLQKMTDLR
QIVTEHVQLLQVIKKTETDMSLHPLLQEIYKDLY

Sequence of entity 2 (B), FASTA

>6MS7_2 PGC1 LXXLL motif (chains B)
PSLLKKLLLAP

Ligands and cofactors

ID	Name	Formula	Copies
V77	{[(1S)-1-(4-chlorophenyl)octyl]oxy}acetic acid	C16 H23 Cl O3	2

Primary citation

Identification and structural insight of an effective PPAR gamma modulator with improved therapeutic index for anti-diabetic drug discovery. Jiang, H., Zhou, X.E., Shi, J. et al. Chem Sci (2020) 11:2260-2268. DOI 10.1039/c9sc05487a · 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…
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…
9F7X 1.63 Å, Human PPARgamma ligand binding domain in complex with co-activator 1alpha peptide and…

Browse structure collections

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