Complex 8yoo
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 | 2.00 |
| System mass | 3842.67 kDa |
| Deposition year | 2024 |
| Molecule type | RNA/Protein |
| # RNA entities | 1 |
| Organism | Homo |
| RCSB PDB Entry | 8yoo |
| Reference | Li Xiang, Wang Mengjiao, Denk Timo, Buschauer Robert, Li Yi, Beckmann Roland, Cheng Jingdong. 2024. Structural basis for differential inhibition of eukaryotic ribosomes by tigecycline Nature Communications |
| Equivalence Class |
NR_all_65061.63,
NR_all_46995.72
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 | T1C |
| Residue | . / 5309 |
| Chain | DK / L5 |
| Non-redundant | True |
| Interacting RNA chains | A/L5 |
| RNA environment detailled | ion, other |
| RNA environment global | RNA/Other |
| RNA family chains | A/L5: rRNA |
| RNA family global | rRNA |
| Volume | 299.10 Å3 |
| Hydrophobicity | 0.185 |
| Hydrophilicity | 1.347 |
| Buriedness | 0.675 |
| Don/acc character | 0.643 |
| SiteScore | 1.135 |
| D Score | 0.906 |
| Kd | — |
| Compound | T1C |
| Residue | . / 5310 |
| Chain | EK / L5 |
| Non-redundant | True |
| Interacting RNA chains | A/L5 |
| RNA environment detailled | ion, other |
| RNA environment global | RNA/Other |
| RNA family chains | A/L5: rRNA |
| RNA family global | rRNA |
| Volume | 355.35 Å3 |
| Hydrophobicity | 0.098 |
| Hydrophilicity | 1.602 |
| Buriedness | 0.684 |
| Don/acc character | 0.722 |
| SiteScore | 0.657 |
| D Score | 0.790 |
| Kd | — |
| Compound | T1C |
| Residue | . / 5311 |
| Chain | FK / L5 |
| Non-redundant | True |
| Interacting RNA chains | A/L5, C/L8 |
| RNA environment detailled | ion |
| RNA environment global | RNA |
| RNA family chains | A/L5: rRNA, C/L8: rRNA |
| RNA family global | rRNA |
| Volume | 343.34 Å3 |
| Hydrophobicity | 0.112 |
| Hydrophilicity | 1.437 |
| Buriedness | 0.690 |
| Don/acc character | 0.773 |
| SiteScore | 1.059 |
| D Score | 0.776 |
| Kd | — |
| Compound | T1C |
| Residue | . / 5312 |
| Chain | GK / L5 |
| Non-redundant | True |
| Interacting RNA chains | A/L5 |
| RNA environment detailled | ion |
| RNA environment global | RNA |
| RNA family chains | A/L5: rRNA |
| RNA family global | rRNA |
| Volume | 350.55 Å3 |
| Hydrophobicity | 0.119 |
| Hydrophilicity | 1.562 |
| Buriedness | 0.677 |
| Don/acc character | 0.777 |
| SiteScore | 0.986 |
| D Score | 0.837 |
| Kd | — |
| Compound | T1C |
| Residue | . / 5313 |
| Chain | HK / L5 |
| Non-redundant | True |
| Interacting RNA chains | A/L5 |
| RNA environment detailled | RNA-only |
| RNA environment global | RNA |
| RNA family chains | A/L5: rRNA |
| RNA family global | rRNA |
| Volume | - |
| Hydrophobicity | - |
| Hydrophilicity | - |
| Buriedness | - |
| Don/acc character | - |
| SiteScore | - |
| D Score | - |
| Kd | — |
| Compound | T1C |
| Residue | . / 1930 |
| Chain | IM / S2 |
| Non-redundant | True |
| Interacting RNA chains | VA/S2 |
| RNA environment detailled | ion |
| RNA environment global | RNA |
| RNA family chains | VA/S2: rRNA |
| RNA family global | rRNA |
| Volume | 275.09 Å3 |
| Hydrophobicity | 0.063 |
| Hydrophilicity | 1.171 |
| Buriedness | 0.708 |
| Don/acc character | 2.275 |
| SiteScore | 1.111 |
| D Score | 0.925 |
| Kd | — |