Research workbench
Ligand binding domain of human ppar gamma in complex with amorfrutin 2
Analyse Ligand binding domain of human ppar gamma in complex with amorfrutin 2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4A4W
- Type
- protein
- Length
- 527 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peroxisome proliferator-activated receptor gamma
- UniProt
- P37231
- Ligands
- YFB
- Pockets
- 7 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 66% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Peroxisome proliferator-activated receptor gamma | protein | 263 | 66% helix, 5% strand | P37231 |
| B | Peroxisome proliferator-activated receptor gamma | protein | 264 | 66% helix, 5% strand | P37231 |
Ligands and binding sites
- YFB · Amorfrutin B · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 497 | 0.81 | 0.87 | 62 | YFB |
| 2 | 437 | 0.76 | 0.85 | 50 | YFB |
| 3 | 315 | 0.68 | 0.82 | 26 | empty |
| 4 | 293 | 0.57 | 0.77 | 30 | empty |
| 5 | 110 | 0.56 | 0.84 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 975 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 4A4W · Ligand binding domain of human PPAR gamma in complex with amorfrutin B · 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 4A4W · PDBe 4A4W · UniProt P37231
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