Research workbench
Crystal structure of hppargamma ligand binding domain complexed with rosiglitazone-based fluorescence probe
Analyse Crystal structure of hppargamma ligand binding domain complexed with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7EFQ
- Type
- protein
- Length
- 511 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peroxisome proliferator-activated receptor gamma
- UniProt
- P37231
- Ligands
- J3F
- Pockets
- 9 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 65% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Peroxisome proliferator-activated receptor gamma | protein | 256 | 67% helix, 5% strand | P37231 |
| B | Peroxisome proliferator-activated receptor gamma | protein | 255 | 63% helix, 5% strand | P37231 |
Ligands and binding sites
- J3F · (5S)-5-[[4-[2-[[7-(diethylamino)-2-oxidanylidene-chromen-4-yl]-methyl-amino]ethoxy]phenyl]methyl]-1,3-thiazolidine-2,4-dione · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 491 | 0.80 | 0.87 | 63 | empty |
| 2 | 449 | 0.79 | 0.86 | 50 | J3F |
| 3 | 105 | 0.58 | 0.86 | 20 | empty |
| 4 | 114 | 0.54 | 0.83 | 16 | empty |
| 5 | 256 | 0.53 | 0.76 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 943 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 7EFQ · Crystal structure of hPPARgamma ligand binding domain complexed with rosiglitazone-based… · 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 7EFQ · PDBe 7EFQ · UniProt P37231
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