Research workbench
Ligand binding domain of human ppar-gamma in complex with the agonist pioglitazone
Analyse Ligand binding domain of human ppar-gamma in complex with the agonist… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2XKW
- Type
- protein
- Length
- 517 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peroxisome proliferator-activated receptor gamma
- UniProt
- P37231
- Ligands
- P1B
- Pockets
- 9 · best druggability 0.80
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 | 261 | 66% helix, 5% strand | P37231 |
| B | Peroxisome proliferator-activated receptor gamma | protein | 256 | 69% helix, 5% strand | P37231 |
Ligands and binding sites
- P1B · (5R)-5-{4-[2-(5-ethylpyridin-2-yl)ethoxy]benzyl}-1,3-thiazolidine-2,4-dione · ligand · 2 copies · chains A, B
- PE4 · 2-{2-[2-(2-{2-[2-(2-ethoxy-ethoxy)-ethoxy]-ethoxy}-ethoxy)-ethoxy]-ethoxy}-ethanol · additive · chains A
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 677 | 0.80 | 0.84 | 69 | P1B |
| 2 | 422 | 0.76 | 0.85 | 53 | P1B |
| 3 | 112 | 0.54 | 0.83 | 17 | empty |
| 4 | 103 | 0.49 | 0.81 | 17 | empty |
| 5 | 218 | 0.48 | 0.75 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 1006 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 2XKW · Ligand binding domain of human ppar-gamma in complex with the agonist pioglitazone · 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 2XKW · PDBe 2XKW · UniProt P37231
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