Complex 8k2a
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 | 2.90 |
| System mass | 2889.20 kDa |
| Deposition year | 2023 |
| Molecule type | RNA/Protein |
| # RNA entities | 1 |
| Organism | Homo |
| RCSB PDB Entry | 8k2a |
| 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_12763.37,
NR_all_93855.32
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 | . / 1706 |
| Chain | GG / L1 |
| Non-redundant | True |
| Interacting RNA chains | A/L1 |
| RNA environment detailled | ion |
| RNA environment global | RNA |
| RNA family chains | A/L1: rRNA |
| RNA family global | rRNA |
| Volume | 362.55 Å3 |
| Hydrophobicity | 0.724 |
| Hydrophilicity | 0.819 |
| Buriedness | 0.699 |
| Don/acc character | 4.299 |
| SiteScore | 1.193 |
| D Score | 1.093 |
| Kd | — |
| Compound | T1C |
| Residue | . / 1707 |
| Chain | HG / L1 |
| Non-redundant | True |
| Interacting RNA chains | A/L1 |
| RNA environment detailled | ion |
| RNA environment global | RNA |
| RNA family chains | A/L1: rRNA |
| RNA family global | rRNA |
| Volume | 597.85 Å3 |
| Hydrophobicity | 0.272 |
| Hydrophilicity | 0.989 |
| Buriedness | 0.697 |
| Don/acc character | 2.310 |
| SiteScore | 1.160 |
| D Score | 1.036 |
| Kd | — |
| Compound | T1C |
| Residue | . / 1034 |
| Chain | EI / S1 |
| Non-redundant | True |
| Interacting RNA chains | EC/S1 |
| RNA environment detailled | ion |
| RNA environment global | RNA |
| RNA family chains | EC/S1: rRNA |
| RNA family global | rRNA |
| Volume | 182.13 Å3 |
| Hydrophobicity | 0.215 |
| Hydrophilicity | 1.114 |
| Buriedness | 0.735 |
| Don/acc character | 1.542 |
| SiteScore | 0.749 |
| D Score | 0.716 |
| Kd | — |
| Compound | T1C |
| Residue | . / 1035 |
| Chain | FI / S1 |
| Non-redundant | True |
| Interacting RNA chains | EC/S1 |
| RNA environment detailled | protein |
| RNA environment global | RNA/Protein |
| RNA family chains | EC/S1: rRNA |
| RNA family global | rRNA |
| Volume | - |
| Hydrophobicity | - |
| Hydrophilicity | - |
| Buriedness | - |
| Don/acc character | - |
| SiteScore | - |
| D Score | - |
| Kd | — |