Research workbench
Crystal structure of ppargamma ligand binding domain in complex with TRAP220 peptide and agonist rosiglitazone
Analyse Crystal structure of ppargamma ligand binding domain in complex with TRAP220… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6ONJ
- Type
- protein
- Length
- 272 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peroxisome proliferator-activated receptor gamma; Mediator of RNA polymerase II…
- UniProt
- P37231, Q15648
- Ligands
- BRL
- Pockets
- 2 · best druggability 0.83
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 | 258 | 69% helix, 5% strand | P37231 |
| C | Mediator of RNA polymerase II transcription subunit 1, TRAP220 coactivator peptide | protein | 14 | 57% helix, 0% strand | Q15648 |
Ligands and binding sites
- BRL · 2,4-thiazolidiinedione, 5-[[4-[2-(methyl-2-pyridinylamino)ethoxy]phenyl]methyl]-(9CL) · 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 | 443 | 0.83 | 0.90 | 54 | BRL |
| 2 | 51 | 0.28 | 0.75 | 11 | empty |
Interfaces
1 interface between chains.
- A–C · 752 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 6ONJ · Crystal structure of PPARgamma ligand binding domain in complex with TRAP220 peptide and… · the same entry in another collection · chain A against A, TM-score 1.00
- Q15648 · AlphaFold monomer V2.0 prediction for mediator of RNA polymerase II transcription subunit… · a predicted model of the same protein · chain C against A, TM-score 0.62
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 Q15648
- Elsewhere: RCSB PDB 6ONJ · PDBe 6ONJ · UniProt P37231 · UniProt Q15648
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