3V9V: PPARgamma-LBD

Crystal structure of the PPARgamma-LBD complexed with a cercosporamide derivative modulator. Determined by X-ray diffraction at 1.6 Å resolution. Released 1 Feb 2012.

Method: X-ray diffraction
Resolution: 1.6 Å
Organism: Homo sapiens
Chains: 2
Atoms: 2,360
Mol. weight: 35.05 kDa
Ligands: 21L
Released: 1 Feb 2012

Explore 3V9V in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3V9V contains 14 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: 13 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	208-225	18
α-helix	230-237	8
α-helix	244-246	3
β-strand	247-249	3	1
α-helix	252-257	6
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	350-354	5
α-helix	361-375	15
α-helix	381-392	12
α-helix	403-424	22
α-helix	431-457	27
α-helix	467-473	7

Chain C: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	8-14	7

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Peroxisome proliferator-activated receptor gamma	A	protein	283	Homo sapiens	P37231 (AlphaFold model)
Peptide from Peroxisome proliferator-activated receptor gamma coactivator 1-alpha	C	protein	19	Homo sapiens	Q9UBK2 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>3V9V_1 Peroxisome proliferator-activated receptor gamma (chains A)
MRGSHHHHHHGPESADLRALAKHLYDSYIKSFPLTKAKARAILTGKTTDKSPFVIYDMNS
LMMGEDKIKFKHITPLQEQSKEVAIRIFQGCQFRSVEAVQEITEYAKSIPGFVNLDLNDQ
VTLLKYGVHEIIYTMLASLMNKDGVLISEGQGFMTREFLKSLRKPFGDFMEPKFEFAVKF
NALELDDSDLAIFIAVIILSGDRPGLLNVKPIEDIQDNLLQALELQLKLNHPESSQLFAK
LLQKMTDLRQIVTEHVQLLQVIKKTETDMSLHPLLQEIYKDLY

Sequence of entity 2 (C), FASTA

>3V9V_2 Peptide from Peroxisome proliferator-activated receptor gamma coactivator 1-alpha (chains C)
QEAEEPSLLKKLLLAPANT

Ligands and cofactors

ID	Name	Formula	Copies
21L	methyl 3-{4-[({[(9aS)-8-acetyl-1,7-dihydroxy-3-methoxy-9a-methyl-9-oxo-9,9a-dih…	C32 H29 N O9	1

Primary citation

Substituents at the naphthalene C3 position of (-)-Cercosporamide derivatives significantly affect the maximal efficacy as PPAR(gamma) partial agonists. Furukawa, A., Arita, T., Fukuzaki, T. et al. Bioorg Med Chem Lett (2011) 22:1348-1351. DOI 10.1016/j.bmcl.2011.12.066 · 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…
9F7X 1.63 Å, Human PPARgamma ligand binding domain in complex with co-activator 1alpha peptide and…

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