MolNFT v1 · #141416 · protein
Crystal structure of the ppargamma-lbd complexed with compound ds-6930
5Z6S · Peroxisome proliferator-activated receptor gamma: “Crystal structure of the ppargamma-lbd complexed with compound ds-6930”. X-ray diffraction, 2 ligands (RTF, CL), 3 pockets (best druggability 0.74). MolNFT v1 #141416 on GenesisL1…
- PDB
- 5Z6S
- Type
- protein
- Length
- 270 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peroxisome proliferator-activated receptor gamma; Peptide from peroxisome…
- UniProt
- P37231, Q9UBK2
- Ligands
- RTF, CL
- Pockets
- 3 · best druggability 0.74
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 | 260 | 66% helix, 5% strand | P37231 |
| C | Peptide from peroxisome proliferator-activated receptor gamma coactivator 1-alpha | protein | 10 | 70% helix, 0% strand | Q9UBK2 |
Ligands and binding sites
- RTF · 3-[[6-(3,5-dimethylpyridin-2-yl)oxy-1-methyl-benzimidazol-2-yl]methoxy]benzoic acid · ligand · chains A
- CL · Chloride ion · ion · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 373 | 0.74 | 0.84 | 49 | RTF |
| 2 | 56 | 0.37 | 0.79 | 12 | empty |
| 3 | 55 | 0.32 | 0.77 | 16 | CL |
Interfaces
1 interface between chains.
- A–C · 538 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 5Z6S · Crystal structure of the PPARgamma-LBD complexed with compound DS-6930 · the same entry in another collection · chain C against C, TM-score 1.00
- Q9UBK2 · AlphaFold monomer V2.0 prediction for peroxisome proliferator- activated receptor gamma… · a predicted model of the same protein · chain C against A, TM-score 0.82
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
- Every structure of UniProt Q9UBK2
- Elsewhere: RCSB PDB 5Z6S · PDBe 5Z6S · UniProt P37231 · UniProt Q9UBK2
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