Complex 8ev6
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 | X-ray |
| Experimental resolution | 2.95 |
| System mass | 4563.75 kDa |
| Deposition year | 2022 |
| Molecule type | RNA/Protein |
| # RNA entities | 1 |
| Organism | Thermus |
| RCSB PDB Entry | 8ev6 |
| Reference | Seely Savannah M., Parajuli Narayan P., De Tarafder Arindam, Ge Xueliang, Sanyal Suparna, Gagnon Matthieu G.. 2023. Molecular basis of the pleiotropic effects by the antibiotic amikacin on the ribosome Nature Communications |
| Equivalence Class |
NR_all_35542.167,
NR_all_65795.87,
NR_all_97519.80
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 | AKN |
| Residue | . / 3936 |
| Chain | HNA / 1A |
| Non-redundant | True |
| Interacting RNA chains | A/1A, CB/1x |
| RNA environment detailled | ion |
| RNA environment global | RNA |
| RNA family chains | A/1A: rRNA, CB/1x: tRNA |
| RNA family global | multiple |
| Volume | 630.43 Å3 |
| Hydrophobicity | 0.088 |
| Hydrophilicity | 1.803 |
| Buriedness | 0.710 |
| Don/acc character | 0.601 |
| SiteScore | 1.158 |
| D Score | 0.778 |
| Kd | — |
| Compound | AKN |
| Residue | . / 3937 |
| Chain | INA / 1A |
| Non-redundant | True |
| Interacting RNA chains | A/1A |
| RNA environment detailled | protein, ion |
| RNA environment global | RNA/Protein |
| RNA family chains | A/1A: rRNA |
| RNA family global | rRNA |
| Volume | 407.14 Å3 |
| Hydrophobicity | 0.000 |
| Hydrophilicity | 2.794 |
| Buriedness | 0.737 |
| Don/acc character | 0.393 |
| SiteScore | 1.026 |
| D Score | 0.471 |
| Kd | — |
| Compound | AKN |
| Residue | . / 202 |
| Chain | MPA / 1O |
| Non-redundant | True |
| Interacting RNA chains | A/1A, FA/1a |
| RNA environment detailled | protein, ion |
| RNA environment global | RNA/Protein |
| RNA family chains | A/1A: rRNA, FA/1a: rRNA |
| RNA family global | rRNA |
| Volume | 616.03 Å3 |
| Hydrophobicity | 0.054 |
| Hydrophilicity | 1.796 |
| Buriedness | 0.674 |
| Don/acc character | 0.727 |
| SiteScore | 0.984 |
| D Score | 0.759 |
| Kd | — |
| Compound | AKN |
| Residue | . / 1913 |
| Chain | BDB / 1a |
| Non-redundant | True |
| Interacting RNA chains | FA/1a |
| RNA environment detailled | ion |
| RNA environment global | RNA |
| RNA family chains | FA/1a: rRNA |
| RNA family global | rRNA |
| Volume | 628.38 Å3 |
| Hydrophobicity | 0.029 |
| Hydrophilicity | 1.357 |
| Buriedness | 0.701 |
| Don/acc character | 1.654 |
| SiteScore | 1.002 |
| D Score | 0.918 |
| Kd | — |
| Compound | AKN |
| Residue | . / 1914 |
| Chain | CDB / 1a |
| Non-redundant | True |
| Interacting RNA chains | FA/1a |
| RNA environment detailled | protein |
| RNA environment global | RNA/Protein |
| RNA family chains | FA/1a: rRNA |
| RNA family global | rRNA |
| Volume | 300.81 Å3 |
| Hydrophobicity | 0.051 |
| Hydrophilicity | 0.980 |
| Buriedness | 0.672 |
| Don/acc character | 1.768 |
| SiteScore | 0.799 |
| D Score | 0.581 |
| Kd | — |
| Compound | AKN |
| Residue | . / 3576 |
| Chain | BBC / 2A |
| Non-redundant | True |
| Interacting RNA chains | EB/2A, GD/2x |
| RNA environment detailled | RNA-only |
| RNA environment global | RNA |
| RNA family chains | EB/2A: rRNA, GD/2x: tRNA |
| RNA family global | multiple |
| Volume | 691.49 Å3 |
| Hydrophobicity | 0.192 |
| Hydrophilicity | 1.198 |
| Buriedness | 0.706 |
| Don/acc character | 0.894 |
| SiteScore | 1.155 |
| D Score | 0.973 |
| Kd | — |
| Compound | AKN |
| Residue | . / 202 |
| Chain | GCC / 2O |
| Non-redundant | True |
| Interacting RNA chains | JC/2a, EB/2A |
| RNA environment detailled | protein |
| RNA environment global | RNA/Protein |
| RNA family chains | EB/2A: rRNA, JC/2a: rRNA |
| RNA family global | rRNA |
| Volume | 637.64 Å3 |
| Hydrophobicity | 0.096 |
| Hydrophilicity | 1.317 |
| Buriedness | 0.691 |
| Don/acc character | 1.302 |
| SiteScore | 0.996 |
| D Score | 0.926 |
| Kd | — |
| Compound | AKN |
| Residue | . / 1911 |
| Chain | XOC / 2a |
| Non-redundant | True |
| Interacting RNA chains | JC/2a |
| RNA environment detailled | RNA-only |
| RNA environment global | RNA |
| RNA family chains | JC/2a: rRNA |
| RNA family global | rRNA |
| Volume | 105.99 Å3 |
| Hydrophobicity | 0.037 |
| Hydrophilicity | 0.871 |
| Buriedness | 0.553 |
| Don/acc character | 3.866 |
| SiteScore | 0.761 |
| D Score | 0.571 |
| Kd | — |