6PDZ: PPARgamma ligand binding domain

Name: PDB 6PDZ: Crystal structure of PPARgamma ligand binding domain in complex with SMRT peptide and inverse agonist T0070907
Published: 2020-03-04
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: transcription

Crystal structure of PPARgamma ligand binding domain in complex with SMRT peptide and inverse agonist T0070907. Determined by X-ray diffraction at 2.1 Å resolution. Released 4 Mar 2020.

Method: X-ray diffraction
Resolution: 2.1 Å
Organism: Homo sapiens
Chains: 4
Atoms: 4,918
Mol. weight: 68.65 kDa
Ligands: EEY
Released: 4 Mar 2020

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

Secondary structure: helices and β-sheets

6PDZ contains 33 α-helices and 8 β-strands across 4 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: 16 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	2
α-helix	252-257	6
α-helix	259-262	4
α-helix	283-288	6
α-helix	290-301	12
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	350-355	6
α-helix	360-362	3
α-helix	365-376	12
α-helix	381-392	12
α-helix	403-424	22
α-helix	431-457	27
α-helix	466-473	8

Chain B: 15 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	206-225	20
α-helix	230-237	8
β-strand	247-249	3	1
α-helix	252-258	7
α-helix	276-287	12
α-helix	290-301	12
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	357	1
α-helix	360-362	3
α-helix	365-376	12
α-helix	381-392	12
α-helix	403-424	22
α-helix	431-457	27
α-helix	467-474	8

Chains C and D: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	2340-2349	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Peroxisome proliferator-activated receptor gamma	A, B	protein	275	Homo sapiens	P37231 (AlphaFold model)
Nuclear receptor corepressor 2	C, D	protein	22	Homo sapiens	Q9Y618 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>6PDZ_1 Peroxisome proliferator-activated receptor gamma (chains A, B)
QLNPESADLRALAKHLYDSYIKSFPLTKAKARAILTGKTTDKSPFVIYDMNSLMMGEDKI
KFKHITPLQEQSKEVAIRIFQGCQFRSVEAVQEITEYAKSIPGFVNLDLNDQVTLLKYGV
HEIIYTMLASLMNKDGVLISEGQGFMTREFLKSLRKPFGDFMEPKFEFAVKFNALELDDS
DLAIFIAVIILSGDRPGLLNVKPIEDIQDNLLQALELQLKLNHPESSQLFAKLLQKMTDL
RQIVTEHVQLLQVIKKTETDMSLHPLLQEIYKDLY

Sequence of entity 2 (C, D), FASTA

>6PDZ_2 Nuclear receptor corepressor 2 (chains C, D)
TNMGLEAIIRKALMGKYDQWEE

Ligands and cofactors

ID	Name	Formula	Copies
EEY	2-chloro-5-nitro-N-(pyridin-4-yl)benzamide	C12 H8 Cl N3 O3	2

Primary citation

A molecular switch regulating transcriptional repression and activation of PPAR gamma. Shang, J., Mosure, S.A., Zheng, J. et al. Nat Commun (2020) 11:956-956. DOI 10.1038/s41467-020-14750-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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