Research workbench
X-ray crystal structure of ppargamma in the complex with caulophyllogenin
Analyse X-ray crystal structure of ppargamma in the complex with caulophyllogenin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5F9B
- Type
- protein
- Length
- 504 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peroxisome proliferator-activated receptor gamma
- UniProt
- P37231
- Ligands
- 5VN
- Pockets
- 9 · best druggability 0.78
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 | 254 | 67% helix, 5% strand | P37231 |
| B | Peroxisome proliferator-activated receptor gamma | protein | 250 | 66% helix, 5% strand | P37231 |
Ligands and binding sites
- 5VN · Caulophyllogenin · ligand · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 498 | 0.78 | 0.85 | 54 | empty |
| 2 | 491 | 0.75 | 0.83 | 56 | 5VN |
| 3 | 287 | 0.57 | 0.77 | 23 | empty |
| 4 | 123 | 0.54 | 0.82 | 19 | empty |
| 5 | 215 | 0.52 | 0.77 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 1005 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 5F9B · X-ray crystal structure of PPARgamma in the complex with caulophyllogenin · 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 5F9B · PDBe 5F9B · UniProt P37231
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