Research workbench
Crystal structure of the ppargamma-lbd complexed with a cercosporamide derivative modulator
Analyse Crystal structure of the ppargamma-lbd complexed with a cercosporamide… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3V9Y
- Type
- protein
- Length
- 272 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peroxisome proliferator-activated receptor gamma; Peptide from nuclear receptor…
- UniProt
- P37231, Q15788
- Ligands
- 24L
- Pockets
- 3 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 68% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Peroxisome proliferator-activated receptor gamma | protein | 261 | 68% helix, 5% strand | P37231 |
| B | Peptide from nuclear receptor coactivator 1 | protein | 11 | 73% helix, 0% strand | Q15788 |
Ligands and binding sites
- 24L · 4-{4-[({[(9aS)-8-acetyl-1,7-dihydroxy-3-methoxy-9a-methyl-9-oxo-9,9a-dihydrodibenzo[b,d]furan-4-yl]carbonyl}amino)methyl]naphthalen-2-yl}butanoic acid · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 418 | 0.80 | 0.88 | 50 | 24L |
| 2 | 64 | 0.37 | 0.78 | 18 | empty |
| 3 | 52 | 0.29 | 0.75 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 658 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 3V9Y · Crystal structure of the PPARgamma-LBD complexed with a cercosporamide derivative… · 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
- Every structure of UniProt Q15788
- Elsewhere: RCSB PDB 3V9Y · PDBe 3V9Y · UniProt P37231 · UniProt Q15788
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