Research workbench
Crystal structure of the complex between ppargamma lbd and the ligand NV1346 (3A)
Analyse Crystal structure of the complex between ppargamma lbd and the ligand NV1346… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6T9C
- Type
- protein
- Length
- 499 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peroxisome proliferator-activated receptor gamma
- UniProt
- P37231
- Ligands
- MX8
- Pockets
- 9 · best druggability 0.78
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 | 251 | 68% helix, 5% strand | P37231 |
| B | Peroxisome proliferator-activated receptor gamma | protein | 248 | 65% helix, 5% strand | P37231 |
Ligands and binding sites
- MX8 · 4-hexoxy-~{N}-[(2~{S})-3-methyl-1-(oxidanylamino)-1-oxidanylidene-butan-2-yl]benzamide · 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 | 470 | 0.78 | 0.85 | 51 | MX8 |
| 2 | 525 | 0.78 | 0.84 | 57 | empty |
| 3 | 106 | 0.61 | 0.87 | 21 | empty |
| 4 | 292 | 0.59 | 0.78 | 26 | empty |
| 5 | 212 | 0.53 | 0.77 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 1132 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 6T9C · Crystal structure of the complex between PPARgamma LBD and the ligand NV1346 (3a) · the same entry in another collection · chain A against A, TM-score 1.00
- P37231 · AlphaFold monomer V2.0 prediction for peroxisome proliferator- activated receptor gamma… · a predicted model of the same protein · chain A against A, TM-score 0.99
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 6T9C · PDBe 6T9C · UniProt P37231
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