Research workbench
Crystal structure of the complex between ppargamma lbd and the ligand am-879
Analyse Crystal structure of the complex between ppargamma lbd and the ligand am-879 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6AN1
- Type
- protein
- Length
- 514 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peroxisome proliferator-activated receptor gamma
- UniProt
- P37231
- Ligands
- BKY
- Pockets
- 7 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 66% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Peroxisome proliferator-activated receptor gamma | protein | 261 | 67% helix, 5% strand | P37231 |
| B | Peroxisome proliferator-activated receptor gamma | protein | 253 | 66% helix, 5% strand | P37231 |
Ligands and binding sites
- BKY · 4-({2-[(1,3-dioxo-1,3-dihydro-2H-inden-2-ylidene) methyl]phenoxy}methyl)benzoic acid · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 556 | 0.80 | 0.86 | 57 | BKY |
| 2 | 365 | 0.80 | 0.89 | 40 | empty |
| 3 | 494 | 0.66 | 0.77 | 61 | empty |
| 4 | 270 | 0.63 | 0.81 | 31 | empty |
| 5 | 146 | 0.46 | 0.76 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 1014 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 6AN1 · Crystal structure of the complex between PPARgamma LBD and the ligand AM-879 · 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 6AN1 · PDBe 6AN1 · UniProt P37231
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.