Research workbench
X-ray structure of ppargamma lbd with the ligand NV1380
Analyse X-ray structure of ppargamma lbd with the ligand NV1380 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6QJ5
- 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
- H8R
- Pockets
- 7 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 67% 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
- H8R · (2~{S})-3-methyl-2-[(4-octoxyphenyl)carbonylamino]butanoic 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, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 441 | 0.80 | 0.87 | 53 | H8R |
| 2 | 453 | 0.76 | 0.84 | 50 | empty |
| 3 | 360 | 0.61 | 0.77 | 39 | empty |
| 4 | 107 | 0.53 | 0.83 | 21 | empty |
| 5 | 162 | 0.51 | 0.78 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 958 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 6QJ5 · X-ray structure of PPARgamma LBD with the ligand NV1380 · the same entry in another collection · chain B against B, 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 6QJ5 · PDBe 6QJ5 · UniProt P37231
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