Complex 8xsx
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 | 4076.45 kDa |
| Deposition year | 2024 |
| Molecule type | RNA/Protein |
| # RNA entities | 1 |
| Organism | Homo |
| RCSB PDB Entry | 8xsx |
| 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 | WA/S2, A/L5 |
| RNA environment detailled | ion |
| RNA environment global | RNA |
| RNA family chains | A/L5: rRNA, WA/S2: rRNA |
| RNA family global | rRNA |
| Volume | 281.95 Å3 |
| Hydrophobicity | 0.024 |
| Hydrophilicity | 1.403 |
| Buriedness | 0.632 |
| Don/acc character | 1.193 |
| SiteScore | 0.973 |
| D Score | 0.691 |
| Kd | — |
| Compound | T1C |
| Residue | . / 5313 |
| Chain | MK / L5 |
| Non-redundant | True |
| Interacting RNA chains | C/L8, A/L5 |
| RNA environment detailled | ion |
| RNA environment global | RNA |
| RNA family chains | A/L5: rRNA, C/L8: rRNA |
| RNA family global | rRNA |
| Volume | 393.76 Å3 |
| Hydrophobicity | 0.121 |
| Hydrophilicity | 1.653 |
| Buriedness | 0.692 |
| Don/acc character | 0.706 |
| SiteScore | 1.146 |
| D Score | 0.816 |
| Kd | — |
| Compound | T1C |
| Residue | . / 5314 |
| Chain | NK / 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 | 509.36 Å3 |
| Hydrophobicity | 0.142 |
| Hydrophilicity | 1.600 |
| Buriedness | 0.708 |
| Don/acc character | 0.472 |
| SiteScore | 1.007 |
| D Score | 0.844 |
| Kd | — |
| Compound | T1C |
| Residue | . / 5315 |
| Chain | OK / 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 | 274.06 Å3 |
| Hydrophobicity | 0.010 |
| Hydrophilicity | 1.304 |
| Buriedness | 0.626 |
| Don/acc character | 2.217 |
| SiteScore | 0.952 |
| D Score | 0.890 |
| 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 | 332.71 Å3 |
| Hydrophobicity | 0.633 |
| Hydrophilicity | 0.887 |
| Buriedness | 0.664 |
| Don/acc character | 1.860 |
| SiteScore | 1.007 |
| D Score | 1.049 |
| 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 | 104.96 Å3 |
| Hydrophobicity | 0.023 |
| Hydrophilicity | 1.097 |
| Buriedness | 0.618 |
| Don/acc character | 3.582 |
| SiteScore | 0.594 |
| D Score | 0.502 |
| Kd | — |
| Compound | T1C |
| Residue | . / 101 |
| Chain | WM / CC |
| Non-redundant | True |
| Interacting RNA chains | GC/CC, A/L5 |
| RNA environment detailled | protein |
| RNA environment global | RNA/Protein |
| RNA family chains | A/L5: rRNA, GC/CC: tRNA |
| RNA family global | multiple |
| Volume | 66.20 Å3 |
| Hydrophobicity | 0.197 |
| Hydrophilicity | 0.856 |
| Buriedness | 0.572 |
| Don/acc character | 1.076 |
| SiteScore | 0.538 |
| D Score | 0.474 |
| Kd | — |