Research workbench
Crystal structure of the complex between ppar-gamma and the agonist LT248 (clofibric acid analogue)
Analyse Crystal structure of the complex between ppar-gamma and the agonist LT248… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3CDS
- 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
- GRR
- Pockets
- 8 · best druggability 0.85
Structure
x-ray diffraction · 1 distinct chain · 65% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Peroxisome proliferator-activated receptor gamma | protein | 270 | 65% helix, 5% strand | P37231 |
Ligands and binding sites
- GRR · (2S)-2-(4-ethylphenoxy)-3-phenylpropanoic acid · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 703 | 0.85 | 0.89 | 75 | empty |
| 2 | 665 | 0.85 | 0.88 | 64 | GRR |
| 3 | 356 | 0.63 | 0.79 | 28 | empty |
| 4 | 205 | 0.46 | 0.74 | 24 | empty |
| 5 | 65 | 0.43 | 0.82 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 974 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 3CDS · Crystal structure of the complex between PPAR-gamma and the agonist LT248 (clofibric acid… · 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 3CDS · PDBe 3CDS · UniProt P37231
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