Research workbench
Crystal structure of the complex between ppargamma lbd and the ligand LJ570: structure obtained from crystals of the apo-form soaked for 15 days.
Analyse Crystal structure of the complex between ppargamma lbd and the ligand LJ570… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6F2L
- Type
- protein
- Length
- 514 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peroxisome proliferator-activated receptor gamma
- UniProt
- P37231
- Ligands
- AXY
- Pockets
- 7 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 67% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Peroxisome proliferator-activated receptor gamma | protein | 259 | 68% helix, 5% strand | P37231 |
| B | Peroxisome proliferator-activated receptor gamma | protein | 255 | 65% helix, 5% strand | P37231 |
Ligands and binding sites
- AXY · (2S)-3-(biphenyl-4-yl)-2-(biphenyl-4-yloxy)propanoic 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, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 547 | 0.82 | 0.88 | 61 | empty |
| 2 | 653 | 0.82 | 0.86 | 62 | AXY |
| 3 | 250 | 0.56 | 0.78 | 31 | empty |
| 4 | 196 | 0.56 | 0.79 | 22 | empty |
| 5 | 250 | 0.56 | 0.77 | 25 | empty |
Interfaces
1 interface between chains.
- A–B · 1067 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 6F2L · Crystal structure of the complex between PPARgamma LBD and the ligand LJ570: structure… · 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 6F2L · PDBe 6F2L · UniProt P37231
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