Complex 8aye
Legend
Pocket colors by molecule type
RNA
Protein
DNA
These colors appear when a pocket is selected (the structure fades to show the pocket surface). Colors from the molecule-type palette (RNA / protein / DNA).
System information
| Experimental technique | Electron Microscopy |
| Experimental resolution | 1.96 |
| System mass | 2175.38 kDa |
| Deposition year | 2022 |
| Molecule type | RNA/Protein |
| # RNA entities | 1 |
| Organism | Escherichia |
| RCSB PDB Entry | 8aye |
| Reference | Parajuli Narayan Prasad, Emmerich Andrew, Mandava Chandra Sekhar, Pavlov Michael Y., Sanyal Suparna. 2023. Antibiotic thermorubin tethers ribosomal subunits and impedes A-site interactions to perturb protein synthesis in bacteria Nature Communications |
| Equivalence Class |
NR_all_83717.187,
NR_all_56726.172
BGSU version: 4.52 |
Pockets List
Legend
Cell colors for SiteScore and D Score:
Favourable
Intermediate
Unfavourable
Not available
| Score | Threshold | Meaning |
|---|---|---|
| SiteScore | < 0.8 | Non-drug binding site |
| SiteScore | 0.8 – 1.0 | Potential drug binding site |
| SiteScore | > 1.0 | Promising binding site |
| D Score | < 0.83 | Undruggable |
| D Score | 0.83 – 0.98 | Difficult |
| D Score | > 0.98 | Druggable |
Tick a pocket below to highlight it in the 3D structure above.
| Compound | T8B |
| Residue | . / 1689 |
| Chain | PE / A |
| Non-redundant | True |
| Interacting RNA chains | DA/a, G/A |
| RNA environment detailled | ion |
| RNA environment global | RNA |
| RNA family chains | G/A: rRNA, DA/a: rRNA |
| RNA family global | rRNA |
| Volume | 275.77 Å3 |
| Hydrophobicity | 0.263 |
| Hydrophilicity | 1.412 |
| Buriedness | 0.653 |
| Don/acc character | 0.977 |
| SiteScore | 0.970 |
| D Score | 0.871 |
| Kd | — |