Research workbench
Covalent bond formation between ynone moiety of synthetic fatty acid and hpparg-lbd
Analyse Covalent bond formation between ynone moiety of synthetic fatty acid and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6JEY
- Type
- protein
- Length
- 503 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peroxisome proliferator-activated receptor gamma
- UniProt
- P37231
- Ligands
- EJL
- Pockets
- 8 · best druggability 0.78
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 | 257 | 68% helix, 5% strand | P37231 |
| B | Peroxisome proliferator-activated receptor gamma | protein | 246 | 71% helix, 5% strand | P37231 |
Ligands and binding sites
- EJL · (9Z,12Z,15Z,18Z,21Z)-5-oxidanylidenetetracosa-9,12,15, 18,21-pentaen-6-ynoic acid · ligand · 3 copies · chains A, 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 | 539 | 0.78 | 0.85 | 57 | EJL |
| 2 | 425 | 0.75 | 0.84 | 44 | EJL |
| 3 | 383 | 0.62 | 0.77 | 44 | empty |
| 4 | 261 | 0.58 | 0.78 | 23 | empty |
| 5 | 100 | 0.45 | 0.80 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 965 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 6JEY · Covalent bond formation between y moiety of synthetic fatty acid and hPPARg-LBD · 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 6JEY · PDBe 6JEY · UniProt P37231
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