Research workbench
Hppargamma ligand binding domain in complex with 6-oxoote
Analyse Hppargamma ligand binding domain in complex with 6-oxoote in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2VV4
- Type
- protein
- Length
- 501 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peroxisome proliferator-activated receptor gamma
- UniProt
- P37231
- Ligands
- 6OC, 6OB
- Pockets
- 8 · best druggability 0.79
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 | 254 | 69% helix, 5% strand | P37231 |
| B | Peroxisome proliferator-activated receptor gamma | protein | 247 | 68% helix, 5% strand | P37231 |
Ligands and binding sites
- 6OC · (8R,9Z,12Z)-8-hydroxy-6-oxooctadeca-9,12-dienoic acid · ligand · chains A
- 6OB · (8E,10S,12Z)-10-hydroxy-6-oxooctadeca-8,12-dienoic acid · ligand · 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 537 | 0.79 | 0.85 | 58 | 6OC |
| 2 | 724 | 0.76 | 0.81 | 69 | 6OB |
| 3 | 272 | 0.58 | 0.78 | 26 | empty |
| 4 | 107 | 0.51 | 0.82 | 21 | empty |
| 5 | 141 | 0.50 | 0.79 | 25 | empty |
Interfaces
1 interface between chains.
- A–B · 913 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 2VV4 · hPPARgamma Ligand binding domain in complex with 6-oxoOTE · 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 2VV4 · PDBe 2VV4 · UniProt P37231
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.