Complex 8rri
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 | 2944.82 kDa |
| Deposition year | 2024 |
| Molecule type | RNA/Protein |
| # RNA entities | 1 |
| Organism | Homo |
| RCSB PDB Entry | 8rri |
| Reference | Shao Qiuya, Khawaja Anas, Nguyen Minh Duc, Singh Vivek, Zhang Jingdian, Liu Yong, Nordin Joel, Adori Monika, Axel Innis C., Castro Dopico Xaquin, Rorbach Joanna. 2025. T cell toxicity induced by tigecycline binding to the mitochondrial ribosome Nature Communications |
| Equivalence Class |
NR_all_12763.37,
NR_all_93855.32,
NR_all_83618.5
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 | . / 1701 |
| Chain | SC / AA |
| Non-redundant | True |
| Interacting RNA chains | EC/AA |
| RNA environment detailled | protein, ion |
| RNA environment global | RNA/Protein |
| RNA family chains | EC/AA: rRNA |
| RNA family global | rRNA |
| Volume | 219.18 Å3 |
| Hydrophobicity | 0.135 |
| Hydrophilicity | 1.181 |
| Buriedness | 0.730 |
| Don/acc character | 3.116 |
| SiteScore | 0.678 |
| D Score | 0.633 |
| Kd | — |
| Compound | T1C |
| Residue | . / 3301 |
| Chain | SD / A |
| Non-redundant | True |
| Interacting RNA chains | FC/A |
| RNA environment detailled | ion |
| RNA environment global | RNA |
| RNA family chains | FC/A: rRNA |
| RNA family global | rRNA |
| Volume | 751.86 Å3 |
| Hydrophobicity | 0.128 |
| Hydrophilicity | 1.263 |
| Buriedness | 0.670 |
| Don/acc character | 1.185 |
| SiteScore | 1.132 |
| D Score | 0.931 |
| Kd | — |
| Compound | T1C |
| Residue | . / 3302 |
| Chain | TD / A |
| Non-redundant | True |
| Interacting RNA chains | HC/Ax, FC/A |
| RNA environment detailled | protein, ion |
| RNA environment global | RNA/Protein |
| RNA family chains | FC/A: rRNA, HC/Ax: tRNA |
| RNA family global | multiple |
| Volume | - |
| Hydrophobicity | - |
| Hydrophilicity | - |
| Buriedness | - |
| Don/acc character | - |
| SiteScore | - |
| D Score | - |
| Kd | — |