Complex 8ekc
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 | 2.70 |
| System mass | 2213.17 kDa |
| Deposition year | 2022 |
| Molecule type | RNA/Protein |
| # RNA entities | 1 |
| Organism | Escherichia |
| RCSB PDB Entry | 8ekc |
| Reference | Paranjpe Madhura N, Marina Valeria I, Grachev Aleksandr A, Maviza Tinashe P, Tolicheva Olga A, Paleskava Alena, Osterman Ilya A, Sergiev Petr V, Konevega Andrey L, Polikanov Yury S, Gagnon Matthieu G. 2023. Insights into the molecular mechanism of translation inhibition by the ribosome-targeting antibiotic thermorubin Nucleic Acids Research |
| 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 | . / 3133 |
| Chain | FG / a |
| Non-redundant | True |
| Interacting RNA chains | A/a, Y/A |
| RNA environment detailled | ion |
| RNA environment global | RNA |
| RNA family chains | A/a: rRNA, Y/A: rRNA |
| RNA family global | rRNA |
| Volume | 255.88 Å3 |
| Hydrophobicity | 0.255 |
| Hydrophilicity | 1.029 |
| Buriedness | 0.646 |
| Don/acc character | 1.491 |
| SiteScore | 0.968 |
| D Score | 0.992 |
| Kd | — |