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
- 3V9T
- Type
- protein
- Length
- 268 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peroxisome proliferator-activated receptor gamma; Peptide from peroxisome…
- UniProt
- P37231, Q9UBK2
- Ligands
- 17L
- Pockets
- 2 · best druggability 0.76
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 | 258 | 68% helix, 5% strand | P37231 |
| C | Peptide from peroxisome proliferator-activated receptor gamma coactivator 1-alpha | protein | 10 | 70% helix, 0% strand | Q9UBK2 |
Ligands and binding sites
- 17L · (9aS)-8-acetyl-N-[(3-ethoxynaphthalen-1-yl)methyl]-1,7-dihydroxy-3-methoxy-9a-methyl-9-oxo-9,9a-dihydrodibenzo[b,d]furan-4-carboxamide · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 386 | 0.76 | 0.86 | 50 | 17L |
| 2 | 54 | 0.34 | 0.77 | 12 | empty |
Interfaces
1 interface between chains.
- A–C · 542 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 3V9T · 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
- Q9UBK2 · AlphaFold monomer V2.0 prediction for peroxisome proliferator- activated receptor gamma… · a predicted model of the same protein · chain C against A, TM-score 0.82
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 Q9UBK2
- Elsewhere: RCSB PDB 3V9T · PDBe 3V9T · UniProt P37231 · UniProt Q9UBK2
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.