MolNFT v1 · #149400 · protein

Ppar mutant complex

6FZF · Peroxisome proliferator-activated receptor gamma: “Ppar mutant complex”. X-ray diffraction, 1 ligand (EDK), 7 pockets (best druggability 0.86). MolNFT v1 #149400 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6FZF
Type: protein
Length: 572 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Peroxisome proliferator-activated receptor gamma; Peroxisome proliferator-activated…
UniProt: P37231, Q9UBK2
Ligands: EDK
Pockets: 7 · best druggability 0.86

Structure

x-ray diffraction · 3 distinct chains · 66% helix, 5% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Peroxisome proliferator-activated receptor gamma	protein	271	67% helix, 5% strand	P37231
B	Peroxisome proliferator-activated receptor gamma	protein	275	65% helix, 5% strand	P37231
C, D	Peroxisome proliferator-activated receptor gamma coactivator 1-alpha	protein	13	54% helix, 0% strand	Q9UBK2

Ligands and binding sites

EDK · (2~{S})-3-[4-[2-[methyl(pyridin-2-yl) amino]ethoxy]phenyl]-2-[[2-(phenylcarbonyl) phenyl]amino]propanoic acid · ligand · 2 copies · chains A, B

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	389	0.86	0.94	50	EDK
2	398	0.86	0.94	51	EDK
3	340	0.60	0.78	37	empty
4	261	0.60	0.79	32	empty
5	105	0.43	0.78	17	empty

Interfaces

3 interfaces between chains.

A–B · 811 Å² buried · 10 hydrogen bonds · protein-protein
A–C · 574 Å² buried · 9 hydrogen bonds · protein-protein
B–D · 545 Å² buried · 7 hydrogen bonds · protein-protein

Compared structures

6FZF · PPAR mutant complex · the same entry in another collection · chain A against A, TM-score 1.00
Q9UBK2 · AlphaFold monomer V2.0 prediction for peroxisome proliferator- activated receptor gamma… · a predicted model of the same protein · chain C against A, TM-score 0.53

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt P37231
Every structure of UniProt Q9UBK2
Elsewhere: RCSB PDB 6FZF · PDBe 6FZF · UniProt P37231 · UniProt Q9UBK2

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