Complex 8xsy
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 | 3.00 |
| System mass | 4007.70 kDa |
| Deposition year | 2024 |
| Molecule type | RNA/Protein |
| # RNA entities | 1 |
| Organism | Homo |
| RCSB PDB Entry | 8xsy |
| 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_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 | . / 5311 |
| Chain | KK / 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 | 562.52 Å3 |
| Hydrophobicity | 0.355 |
| Hydrophilicity | 0.959 |
| Buriedness | 0.707 |
| Don/acc character | 1.790 |
| SiteScore | 1.172 |
| D Score | 1.051 |
| Kd | — |
| Compound | T1C |
| Residue | . / 5312 |
| Chain | LK / 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 | 408.51 Å3 |
| Hydrophobicity | 0.070 |
| Hydrophilicity | 1.227 |
| Buriedness | 0.657 |
| Don/acc character | 1.390 |
| SiteScore | 0.631 |
| D Score | 0.886 |
| 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 | 445.90 Å3 |
| Hydrophobicity | 0.151 |
| Hydrophilicity | 1.373 |
| Buriedness | 0.684 |
| Don/acc character | 1.046 |
| SiteScore | 1.141 |
| D Score | 0.903 |
| 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 | 462.36 Å3 |
| Hydrophobicity | 0.102 |
| Hydrophilicity | 1.616 |
| Buriedness | 0.701 |
| Don/acc character | 0.737 |
| SiteScore | 1.002 |
| D Score | 0.834 |
| 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 | 385.53 Å3 |
| Hydrophobicity | 0.070 |
| Hydrophilicity | 1.239 |
| Buriedness | 0.674 |
| Don/acc character | 2.226 |
| SiteScore | 1.134 |
| D Score | 0.941 |
| 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 | 345.74 Å3 |
| Hydrophobicity | 1.059 |
| Hydrophilicity | 0.772 |
| Buriedness | 0.687 |
| Don/acc character | 3.888 |
| SiteScore | 1.045 |
| D Score | 1.101 |
| 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 | 75.80 Å3 |
| Hydrophobicity | 0.093 |
| Hydrophilicity | 0.881 |
| Buriedness | 0.574 |
| Don/acc character | 4.602 |
| SiteScore | 0.609 |
| D Score | 0.563 |
| Kd | — |
| Compound | T1C |
| Residue | . / 101 |
| Chain | SM / 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 | 66.89 Å3 |
| Hydrophobicity | 0.376 |
| Hydrophilicity | 0.699 |
| Buriedness | 0.566 |
| Don/acc character | 1.487 |
| SiteScore | 0.611 |
| D Score | 0.582 |
| Kd | — |