Research workbench
Ligand binding domain of the human peroxisome proliferator activated receptor gamma in complex with a synthetic 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
- 1KNU
- Type
- protein
- Length
- 523 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peroxisome proliferator activated receptor gamma
- UniProt
- P37231
- Ligands
- YPA
- Pockets
- 8 · best druggability 0.83
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 | 265 | 66% helix, 5% strand | P37231 |
| B | Peroxisome proliferator activated receptor gamma | protein | 258 | 68% helix, 5% strand | P37231 |
Ligands and binding sites
- YPA · (S)-3-(4-(2-carbazol-9-yl-ethoxy)-phenyl)-2-ethoxy-propionic acid · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 533 | 0.83 | 0.89 | 56 | YPA |
| 2 | 394 | 0.83 | 0.91 | 52 | empty |
| 3 | 406 | 0.63 | 0.77 | 49 | empty |
| 4 | 119 | 0.59 | 0.85 | 24 | empty |
| 5 | 242 | 0.54 | 0.76 | 25 | empty |
Interfaces
1 interface between chains.
- A–B · 898 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 1KNU · 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 1KNU · PDBe 1KNU · UniProt P37231
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