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Crystal structure of the complex between ppargamma lbd and the LT175(R-enantiomer)

Analyse Crystal structure of the complex between ppargamma lbd and the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3D6D
Type: protein
Length: 540 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Peroxisome proliferator-activated receptor gamma
UniProt: P37231
Ligands: LRG
Pockets: 7 · best druggability 0.84

Structure

x-ray diffraction · 1 distinct chain · 63% helix, 5% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Peroxisome proliferator-activated receptor gamma	protein	270	63% helix, 5% strand	P37231

Ligands and binding sites

LRG · (2S)-2-(biphenyl-4-yloxy)-3-phenylpropanoic acid · ligand · chains A

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	756	0.84	0.87	73	empty
2	563	0.84	0.89	53	LRG
3	346	0.67	0.81	32	empty
4	330	0.56	0.75	41	empty
5	72	0.45	0.81	16	empty

Interfaces

1 interface between chains.

A–B · 987 Å² buried · 11 hydrogen bonds · protein-protein

Compared structures

3D6D · Crystal Structure of the complex between PPARgamma LBD and the LT175(R-enantiomer) · the same entry in another collection · chain A against A, TM-score 1.00

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
Elsewhere: RCSB PDB 3D6D · PDBe 3D6D · UniProt P37231

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