Research workbench
Crystal structure of ppargamma ligand binding domain in complex with tripropyltin
Analyse Crystal structure of ppargamma ligand binding domain in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3PO9
- Type
- protein
- Length
- 510 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peroxisome proliferator-activated receptor gamma
- UniProt
- P37231
- Ligands
- XPT
- Pockets
- 8 · best druggability 0.80
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 | 261 | 66% helix, 5% strand | P37231 |
| B | Peroxisome proliferator-activated receptor gamma | protein | 249 | 69% helix, 5% strand | P37231 |
Ligands and binding sites
- XPT · 1-[chloro(dipropyl)-lambda~4~-sulfanyl]propane · ligand · 2 copies · chains A, B
- PGO · S-1,2-propanediol · additive · 4 copies · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 428 | 0.80 | 0.87 | 52 | XPT |
| 2 | 474 | 0.79 | 0.86 | 52 | XPT, PGO |
| 3 | 498 | 0.63 | 0.76 | 52 | PGO |
| 4 | 145 | 0.58 | 0.83 | 23 | empty |
| 5 | 162 | 0.55 | 0.81 | 28 | empty |
Interfaces
1 interface between chains.
- A–B · 863 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 3PO9 · Crystal structure of PPARgamma ligand binding domain in complex with tripropyltin · 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 3PO9 · PDBe 3PO9 · UniProt P37231
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