Complex 8ev6
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.. . Molecular basis of the pleiotropic effects by the antibiotic amikacin on the ribosome Nature Communications |
| Equivalence Class |
NR_all_35542.165,
NR_all_65795.87,
NR_all_97519.80
BGSU version: 4.48 |
| 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 | — |