MolNFT v1 · #171951 · protein
Crystal structure of the complex between ppargamma lbd and the ligand NV1362 (7A)
6ZLY · Peroxisome proliferator-activated receptor gamma: “Crystal structure of the complex between ppargamma lbd and the ligand NV1362 (7A)”. X-ray diffraction, 1 ligand (QMH), 7 pockets (best druggability 0.78). MolNFT v1 #171951 on…
- PDB
- 6ZLY
- Type
- protein
- Length
- 496 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peroxisome proliferator-activated receptor gamma
- UniProt
- P37231
- Ligands
- QMH
- Pockets
- 7 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 68% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Peroxisome proliferator-activated receptor gamma | protein | 252 | 69% helix, 5% strand | P37231 |
| B | Peroxisome proliferator-activated receptor gamma | protein | 244 | 68% helix, 5% strand | P37231 |
Ligands and binding sites
- QMH · (2~{S})-2-[(4-hexoxyphenyl)carbonylamino]-3-methyl-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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 494 | 0.78 | 0.85 | 56 | QMH |
| 2 | 466 | 0.75 | 0.83 | 56 | empty |
| 3 | 365 | 0.69 | 0.82 | 38 | empty |
| 4 | 109 | 0.57 | 0.85 | 22 | empty |
| 5 | 205 | 0.49 | 0.76 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 1138 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 6ZLY · Crystal structure of the complex between PPARgamma LBD and the ligand NV1362 (7a) · 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 6ZLY · PDBe 6ZLY · UniProt P37231
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