Research workbench
Crystal structure of ppargamma ligand binding domain in complex with tributyltin
Analyse Crystal structure of ppargamma ligand binding domain in complex with tributyltin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3WJ4
- Type
- protein
- Length
- 516 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peroxisome proliferator-activated receptor gamma
- UniProt
- P37231
- Ligands
- TBY
- Pockets
- 5 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 69% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Peroxisome proliferator-activated receptor gamma | protein | 256 | 70% helix, 5% strand | P37231 |
| B | Peroxisome proliferator-activated receptor gamma | protein | 260 | 68% helix, 5% strand | P37231 |
Ligands and binding sites
- TBY · tributylstannanyl · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1009 | 0.82 | 0.83 | 121 | TBY |
| 2 | 489 | 0.78 | 0.85 | 46 | TBY |
| 3 | 144 | 0.64 | 0.86 | 22 | empty |
| 4 | 164 | 0.57 | 0.82 | 27 | empty |
| 5 | 234 | 0.52 | 0.76 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 835 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 3WJ4 · Crystal structure of PPARgamma ligand binding domain in complex with tributyltin · 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 3WJ4 · PDBe 3WJ4 · UniProt P37231
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.