Research workbench
Crystal structure of the PPARgamma-LBD complexed with compound 1l
Analyse Crystal structure of the PPARgamma-LBD complexed with compound 1l in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6IZM
- Type
- protein
- Length
- 276 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.8
- Source
- Homo sapiens; SYNTHETIC CONSTRUCT
- Molecule
- Peroxisome proliferator-activated receptor gamma; Peptide from Peroxisome…
- UniProt
- P37231, Q9UBK2
- Ligands
- B0X
- Pockets
- 2 · best druggability 0.81
Structure
x-ray diffraction · resolution 1.8 · 2 distinct chains · 66% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Peroxisome proliferator-activated receptor gamma | protein | 266 | 66% helix, 5% strand | P37231 |
| C | Peptide from Peroxisome proliferator-activated receptor gamma coactivator 1-alpha | protein | 10 | 70% helix, 0% strand | Q9UBK2 |
Ligands and binding sites
- B0X · 3-[[6-(2,6-dimethylpyridin-3-yl)oxy-1-methyl-benzimidazol-2-yl]methoxy]benzoic acid · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 467 | 0.81 | 0.88 | 59 | B0X |
| 2 | 55 | 0.34 | 0.78 | 12 | empty |
Interfaces
1 interface between chains.
- A–C · 536 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 6IZM · Crystal structure of the ppargamma-lbd complexed with compound 1L · the same entry in another collection · chain A against A, TM-score 1.00
- Q9UBK2 · AlphaFold monomer V2.0 prediction for peroxisome proliferator- activated receptor gamma… · a predicted model of the same protein · chain C against A, TM-score 0.77
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
- Every structure of UniProt Q9UBK2
- Elsewhere: RCSB PDB 6IZM · PDBe 6IZM · UniProt P37231 · UniProt Q9UBK2
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