Research workbench

Ppargamma in complex with a 2-baba compound

Analyse Ppargamma in complex with a 2-baba compound in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1WM0
Type: protein
Length: 282 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Peroxisome proliferator activated receptor gamma; 14-mer from nuclear receptor…
UniProt: Q96J12, Q61026
Ligands: PLB
Pockets: 1 · best druggability 0.85

Structure

x-ray diffraction · 2 distinct chains · 61% helix, 5% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
X	Peroxisome proliferator activated receptor gamma	protein	272	61% helix, 5% strand	Q96J12
Y	14-mer from nuclear receptor coactivator 2	protein	10	60% helix, 0% strand	Q61026

Ligands and binding sites

PLB · 2-[(2,4-dichlorobenzoyl)amino]-5-(pyrimidin-2-yloxy)benzoic acid · ligand · chains X

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

Pockets

1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	353	0.85	0.94	52	PLB

Interfaces

1 interface between chains.

X–Y · 572 Å² buried · 6 hydrogen bonds · protein-protein

Compared structures

1WM0 · PPARgamma in complex with a 2-BABA compound · the same entry in another collection · chain X against X, TM-score 1.00
Q61026 · AlphaFold monomer V2.0 prediction for nuclear receptor coactivator 2 (Q61026) · a predicted model of the same protein · chain Y against A, TM-score 0.67

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 Q96J12
Every structure of UniProt Q61026
Elsewhere: RCSB PDB 1WM0 · PDBe 1WM0 · UniProt Q96J12 · UniProt Q61026

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