Complex 8ev7
System information
| Experimental technique | X-ray |
| Experimental resolution | 2.89 |
| System mass | 4560.66 kDa |
| Deposition year | 2022 |
| Molecule type | RNA/Protein |
| # RNA entities | 1 |
| Organism | Thermus |
| RCSB PDB Entry | 8ev7 |
| 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_65795.87,
NR_all_97519.80
BGSU version: 4.48 |
| Compound | KAN |
| Residue | . / 3933 |
| Chain | ENA / 1A |
| Non-redundant | True |
| Interacting RNA chains | A/1A |
| RNA environment detailled | ion |
| RNA environment global | RNA |
| RNA family chains | A/1A: rRNA |
| RNA family global | rRNA |
| Volume | 443.84 Å3 |
| Hydrophobicity | 0.038 |
| Hydrophilicity | 1.870 |
| Buriedness | 0.697 |
| Don/acc character | 1.033 |
| SiteScore | 1.149 |
| D Score | 0.748 |
| Kd | — |
| Compound | KAN |
| Residue | . / 3934 |
| Chain | FNA / 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 | 483.97 Å3 |
| Hydrophobicity | 0.083 |
| Hydrophilicity | 1.737 |
| Buriedness | 0.670 |
| Don/acc character | 1.032 |
| SiteScore | 1.131 |
| D Score | 0.776 |
| Kd | — |
| Compound | KAN |
| Residue | . / 3935 |
| Chain | GNA / 1A |
| Non-redundant | True |
| Interacting RNA chains | A/1A |
| RNA environment detailled | ion |
| RNA environment global | RNA |
| RNA family chains | A/1A: rRNA |
| RNA family global | rRNA |
| Volume | 684.29 Å3 |
| Hydrophobicity | 0.126 |
| Hydrophilicity | 1.160 |
| Buriedness | 0.745 |
| Don/acc character | 1.661 |
| SiteScore | 1.181 |
| D Score | 1.009 |
| Kd | — |
| Compound | KAN |
| Residue | . / 1955 |
| Chain | FEB / 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 | 725.10 Å3 |
| Hydrophobicity | 0.039 |
| Hydrophilicity | 1.260 |
| Buriedness | 0.690 |
| Don/acc character | 1.404 |
| SiteScore | 0.994 |
| D Score | 0.943 |
| Kd | — |
| Compound | KAN |
| Residue | . / 3568 |
| Chain | ACC / 2A |
| Non-redundant | True |
| Interacting RNA chains | EB/2A |
| RNA environment detailled | ion |
| RNA environment global | RNA |
| RNA family chains | EB/2A: rRNA |
| RNA family global | rRNA |
| Volume | 494.95 Å3 |
| Hydrophobicity | 0.022 |
| Hydrophilicity | 1.670 |
| Buriedness | 0.678 |
| Don/acc character | 1.042 |
| SiteScore | 0.987 |
| D Score | 0.802 |
| Kd | — |
| Compound | KAN |
| Residue | . / 3569 |
| Chain | BCC / 2A |
| Non-redundant | True |
| Interacting RNA chains | EB/2A |
| RNA environment detailled | ion |
| RNA environment global | RNA |
| RNA family chains | EB/2A: rRNA |
| RNA family global | rRNA |
| Volume | 572.81 Å3 |
| Hydrophobicity | 0.083 |
| Hydrophilicity | 1.634 |
| Buriedness | 0.734 |
| Don/acc character | 0.664 |
| SiteScore | 1.174 |
| D Score | 0.848 |
| Kd | — |
| Compound | KAN |
| Residue | . / 1828 |
| Chain | JMC / 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 | 302.53 Å3 |
| Hydrophobicity | 0.105 |
| Hydrophilicity | 0.940 |
| Buriedness | 0.693 |
| Don/acc character | 1.454 |
| SiteScore | 0.860 |
| D Score | 0.849 |
| Kd | — |