Research workbench
Human ppargamma ligand-binding domain in complex with 5-methoxy-indole acetate
Analyse Human ppargamma ligand-binding domain in complex with 5-methoxy-indole acetate in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3ADU
- Type
- protein
- Length
- 520 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peroxisome proliferator-activated receptor gamma
- UniProt
- P37231
- Ligands
- MYI
- Pockets
- 8 · 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 | 259 | 67% helix, 5% strand | P37231 |
| B | Peroxisome proliferator-activated receptor gamma | protein | 261 | 66% helix, 5% strand | P37231 |
Ligands and binding sites
- MYI · (5-methoxy-1H-indol-3-yl)acetic acid · ligand · 5 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 599 | 0.80 | 0.85 | 65 | MYI |
| 2 | 518 | 0.79 | 0.86 | 56 | MYI |
| 3 | 405 | 0.62 | 0.77 | 45 | empty |
| 4 | 126 | 0.58 | 0.85 | 24 | empty |
| 5 | 88 | 0.53 | 0.85 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 1051 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 3ADU · Human PPARgamma ligand-binding domain in complex with 5-methoxy-indole acetate · 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 3ADU · PDBe 3ADU · UniProt P37231
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.