Research workbench
Covalent bond formation of bifunctional ligand with hpparg-lbd
Analyse Covalent bond formation of bifunctional ligand with hpparg-lbd in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5WR1
- 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
- 8XO
- Pockets
- 8 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 68% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Peroxisome proliferator-activated receptor gamma | protein | 257 | 67% helix, 5% strand | P37231 |
| B | Peroxisome proliferator-activated receptor gamma | protein | 246 | 69% helix, 5% strand | P37231 |
Ligands and binding sites
- 8XO · 2-[E-(E-16-azido-2-oxidanylidene-hexadec-3-enylidene) amino]ethanoic 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, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 477 | 0.77 | 0.85 | 57 | 8XO |
| 2 | 558 | 0.77 | 0.83 | 58 | empty |
| 3 | 305 | 0.61 | 0.79 | 25 | empty |
| 4 | 130 | 0.56 | 0.83 | 25 | empty |
| 5 | 107 | 0.54 | 0.84 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 999 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 5WR1 · Covalent bond formation of bifunctional ligand with 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 5WR1 · PDBe 5WR1 · UniProt P37231
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