Research workbench
Crystal structure of the ligand binding domain of human ppar-gamma in complex with an agonist
Analyse Crystal structure of the ligand binding domain of human ppar-gamma in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2F4B
- Type
- protein
- Length
- 542 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peroxisome proliferator-activated receptor gamma
- UniProt
- P37231
- Ligands
- EHA
- Pockets
- 8 · best druggability 0.85
Structure
x-ray diffraction · 1 distinct chain · 66% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Peroxisome proliferator-activated receptor gamma | protein | 271 | 66% helix, 4% strand | P37231 |
Ligands and binding sites
- EHA · (5-{3-[(6-benzoyl-1-propyl-2-naphthyl)oxy]propoxy}-1H-indol-1-yl)acetic 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 | 785 | 0.85 | 0.87 | 69 | EHA |
| 2 | 669 | 0.83 | 0.87 | 76 | empty |
| 3 | 248 | 0.70 | 0.86 | 26 | empty |
| 4 | 260 | 0.56 | 0.77 | 32 | empty |
| 5 | 69 | 0.53 | 0.86 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 858 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 2F4B · Crystal structure of the ligand binding domain of human PPAR-gamma in complex with an… · the same entry in another collection · chain A against A, TM-score 1.00
- P37231 · AlphaFold monomer V2.0 prediction for peroxisome proliferator- activated receptor gamma… · a predicted model of the same protein · chain A against A, TM-score 0.97
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 2F4B · PDBe 2F4B · UniProt P37231
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.