Research workbench
Covalent labeling of hpparg-lbd by turn-on fluorescent probe mediated by conjugate addition and cyclization
Analyse Covalent labeling of hpparg-lbd by turn-on fluorescent probe mediated by… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6JF0
- 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
- EB6, EBF
- Pockets
- 6 · 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 | 257 | 68% helix, 5% strand | P37231 |
| B | Peroxisome proliferator-activated receptor gamma | protein | 246 | 70% helix, 5% strand | P37231 |
Ligands and binding sites
- EB6 · Methyl (2~{S})-3-[4-[3-(4-methoxy-2-oxidanyl-phenyl) prop-2-ynoyloxy]phenyl]-2-[[2-(phenylcarbonyl) phenyl]amino]propanoate · ligand · chains A
- EBF · 7-methoxychromen-2-one · ligand · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 484 | 0.79 | 0.86 | 51 | EB6 |
| 2 | 715 | 0.77 | 0.81 | 64 | EBF |
| 3 | 320 | 0.60 | 0.78 | 26 | empty |
| 4 | 334 | 0.58 | 0.76 | 39 | empty |
| 5 | 86 | 0.39 | 0.77 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 912 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 6JF0 · Covalent labeling of hPPARg-LBD by turn-on fluorescent probe mediated by conjugate… · the same entry in another collection · chain B against B, 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 6JF0 · PDBe 6JF0 · UniProt P37231
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