Research workbench
Ligand binding domain of the human peroxisome proliferator activated receptor gamma in complex with an agonist
Analyse Ligand binding domain of the human peroxisome proliferator activated receptor… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1NYX
- Type
- protein
- Length
- 518 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peroxisome proliferator activated receptor gamma
- UniProt
- P37231
- Ligands
- DRF
- Pockets
- 9 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 62% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Peroxisome proliferator activated receptor gamma | protein | 260 | 62% helix, 5% strand | P37231 |
| B | Peroxisome proliferator activated receptor gamma | protein | 258 | 63% helix, 5% strand | P37231 |
Ligands and binding sites
- DRF · (2S)-2-ethoxy-3-{4-[2-(10H-phenoxazin-10-yl)ethoxy]phenyl}propanoic acid · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 390 | 0.83 | 0.92 | 57 | empty |
| 2 | 531 | 0.79 | 0.85 | 61 | DRF |
| 3 | 475 | 0.74 | 0.83 | 50 | empty |
| 4 | 192 | 0.58 | 0.80 | 21 | empty |
| 5 | 218 | 0.53 | 0.77 | 27 | empty |
Interfaces
1 interface between chains.
- A–B · 1016 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 1NYX · Ligand binding domain of the human peroxisome proliferator activated receptor gamma in… · 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 1NYX · PDBe 1NYX · UniProt P37231
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