Complex 8k2c
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 | 2.40 |
| System mass | 4008.39 kDa |
| Deposition year | 2023 |
| Molecule type | RNA/Protein |
| # RNA entities | 1 |
| Organism | Homo |
| RCSB PDB Entry | 8k2c |
| 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,
NR_all_83098.14
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 | . / 5312 |
| Chain | LK / 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 | 494.26 Å3 |
| Hydrophobicity | 0.214 |
| Hydrophilicity | 1.358 |
| Buriedness | 0.681 |
| Don/acc character | 0.772 |
| SiteScore | 1.139 |
| D Score | 0.906 |
| Kd | — |
| Compound | T1C |
| Residue | . / 5313 |
| Chain | MK / 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 | 289.15 Å3 |
| Hydrophobicity | 0.083 |
| Hydrophilicity | 1.508 |
| Buriedness | 0.656 |
| Don/acc character | 0.730 |
| SiteScore | 0.903 |
| D Score | 0.748 |
| Kd | — |
| Compound | T1C |
| Residue | . / 5314 |
| Chain | NK / 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 | 641.75 Å3 |
| Hydrophobicity | 0.093 |
| Hydrophilicity | 1.348 |
| Buriedness | 0.673 |
| Don/acc character | 1.221 |
| SiteScore | 1.133 |
| D Score | 0.904 |
| Kd | — |
| Compound | T1C |
| Residue | . / 5315 |
| Chain | OK / 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 | 431.49 Å3 |
| Hydrophobicity | 0.154 |
| Hydrophilicity | 1.654 |
| Buriedness | 0.700 |
| Don/acc character | 0.863 |
| SiteScore | 1.001 |
| D Score | 0.821 |
| Kd | — |
| Compound | T1C |
| Residue | . / 5316 |
| Chain | PK / L5 |
| Non-redundant | True |
| Interacting RNA chains | A/L5 |
| RNA environment detailled | other |
| RNA environment global | RNA/Other |
| RNA family chains | A/L5: rRNA |
| RNA family global | rRNA |
| Volume | 311.10 Å3 |
| Hydrophobicity | 0.035 |
| Hydrophilicity | 1.430 |
| Buriedness | 0.665 |
| Don/acc character | 1.788 |
| SiteScore | 0.975 |
| D Score | 0.868 |
| Kd | — |
| Compound | T1C |
| Residue | . / 5317 |
| Chain | QK / L5 |
| Non-redundant | True |
| Interacting RNA chains | A/L5 |
| RNA environment detailled | other |
| RNA environment global | RNA/Other |
| RNA family chains | A/L5: rRNA |
| RNA family global | rRNA |
| Volume | 481.23 Å3 |
| Hydrophobicity | 0.433 |
| Hydrophilicity | 0.943 |
| Buriedness | 0.658 |
| Don/acc character | 2.284 |
| SiteScore | 0.992 |
| D Score | 1.027 |
| Kd | — |
| Compound | T1C |
| Residue | . / 5318 |
| Chain | RK / L5 |
| Non-redundant | True |
| Interacting RNA chains | A/L5 |
| RNA environment detailled | other |
| RNA environment global | RNA/Other |
| RNA family chains | A/L5: rRNA |
| RNA family global | rRNA |
| Volume | 164.30 Å3 |
| Hydrophobicity | 0.020 |
| Hydrophilicity | 1.349 |
| Buriedness | 0.679 |
| Don/acc character | 2.326 |
| SiteScore | 0.831 |
| D Score | 0.707 |
| Kd | — |
| Compound | T1C |
| Residue | . / 1930 |
| Chain | SM / S2 |
| Non-redundant | True |
| Interacting RNA chains | GC/CC, WA/S2 |
| RNA environment detailled | protein |
| RNA environment global | RNA/Protein |
| RNA family chains | GC/CC: tRNA, WA/S2: rRNA |
| RNA family global | multiple |
| Volume | 433.90 Å3 |
| Hydrophobicity | 0.657 |
| Hydrophilicity | 1.283 |
| Buriedness | 0.819 |
| Don/acc character | 0.831 |
| SiteScore | 1.081 |
| D Score | 1.013 |
| Kd | — |
| Compound | T1C |
| Residue | . / 101 |
| Chain | XM / CC |
| Non-redundant | True |
| Interacting RNA chains | A/L5, GC/CC |
| RNA environment detailled | protein |
| RNA environment global | RNA/Protein |
| RNA family chains | A/L5: rRNA, GC/CC: tRNA |
| RNA family global | multiple |
| Volume | 72.03 Å3 |
| Hydrophobicity | 0.212 |
| Hydrophilicity | 0.709 |
| Buriedness | 0.552 |
| Don/acc character | 1.164 |
| SiteScore | 0.526 |
| D Score | 0.476 |
| Kd | — |