Complex 5ndg
System information
| Experimental technique | X-ray |
| Experimental resolution | 3.70 |
| System mass | 6233.17 kDa |
| Deposition year | 2017 |
| Molecule type | RNA/Protein |
| # RNA entities | 1 |
| Organism | Saccharomyces |
| RCSB PDB Entry | 5ndg |
| Reference | Prokhorova Irina, Altman Roger B., Djumagulov Muminjon, Shrestha Jaya P., Urzhumtsev Alexandre, Ferguson Angelica, Chang Cheng-Wei Tom, Yusupov Marat, Blanchard Scott C., Yusupova Gulnara. . Aminoglycoside interactions and impacts on the eukaryotic ribosome Proceedings of the National Academy of Sciences |
| Equivalence Class |
NR_all_90506.85,
NR_all_03510.74
BGSU version: 4.49 |
| Compound | GET |
| Residue | . / 2012 |
| Chain | KJ / 2 |
| Non-redundant | True |
| Interacting RNA chains | A/2 |
| RNA environment detailled | RNA-only |
| RNA environment global | RNA |
| RNA family chains | A/2: rRNA |
| RNA family global | rRNA |
| Volume | 48.71 Å3 |
| Hydrophobicity | 0.128 |
| Hydrophilicity | 1.208 |
| Buriedness | 0.569 |
| Don/acc character | 1.263 |
| SiteScore | 0.776 |
| D Score | 0.519 |
| Kd | — |
| Compound | GET |
| Residue | . / 2013 |
| Chain | LJ / 2 |
| Non-redundant | True |
| Interacting RNA chains | A/2 |
| RNA environment detailled | protein, ion |
| RNA environment global | RNA/Protein |
| RNA family chains | A/2: rRNA |
| RNA family global | rRNA |
| Volume | 534.05 Å3 |
| Hydrophobicity | 0.179 |
| Hydrophilicity | 1.587 |
| Buriedness | 0.788 |
| Don/acc character | 1.296 |
| SiteScore | 1.210 |
| D Score | 0.895 |
| Kd | — |
| Compound | GET |
| Residue | . / 2014 |
| Chain | MJ / 2 |
| Non-redundant | True |
| Interacting RNA chains | A/2 |
| RNA environment detailled | protein |
| RNA environment global | RNA/Protein |
| RNA family chains | A/2: rRNA |
| RNA family global | rRNA |
| Volume | 459.62 Å3 |
| Hydrophobicity | 0.108 |
| Hydrophilicity | 0.971 |
| Buriedness | 0.703 |
| Don/acc character | 1.863 |
| SiteScore | 1.097 |
| D Score | 0.956 |
| Kd | — |
| Compound | GET |
| Residue | . / 3808 |
| Chain | SZ / 1 |
| Non-redundant | True |
| Interacting RNA chains | JA/1 |
| RNA environment detailled | protein, ion |
| RNA environment global | RNA/Protein |
| RNA family chains | JA/1: rRNA |
| RNA family global | rRNA |
| Volume | 228.78 Å3 |
| Hydrophobicity | 0.000 |
| Hydrophilicity | 1.226 |
| Buriedness | 0.685 |
| Don/acc character | 1.105 |
| SiteScore | 0.952 |
| D Score | 0.709 |
| Kd | — |
| Compound | GET |
| Residue | . / 3809 |
| Chain | TZ / 1 |
| Non-redundant | True |
| Interacting RNA chains | JA/1 |
| RNA environment detailled | ion, other |
| RNA environment global | RNA/Other |
| RNA family chains | JA/1: rRNA |
| RNA family global | rRNA |
| Volume | 630.43 Å3 |
| Hydrophobicity | 0.140 |
| Hydrophilicity | 1.630 |
| Buriedness | 0.776 |
| Don/acc character | 1.108 |
| SiteScore | 1.202 |
| D Score | 0.874 |
| Kd | — |
| Compound | GET |
| Residue | . / 3810 |
| Chain | UZ / 1 |
| Non-redundant | True |
| Interacting RNA chains | JA/1, LA/4 |
| RNA environment detailled | RNA-only |
| RNA environment global | RNA |
| RNA family chains | JA/1: rRNA, LA/4: rRNA |
| RNA family global | rRNA |
| Volume | 743.62 Å3 |
| Hydrophobicity | 0.252 |
| Hydrophilicity | 1.154 |
| Buriedness | 0.696 |
| Don/acc character | 1.325 |
| SiteScore | 1.149 |
| D Score | 0.982 |
| Kd | — |
| Compound | GET |
| Residue | . / 3811 |
| Chain | VZ / 1 |
| Non-redundant | True |
| Interacting RNA chains | JA/1 |
| RNA environment detailled | protein, ion |
| RNA environment global | RNA/Protein |
| RNA family chains | JA/1: rRNA |
| RNA family global | rRNA |
| Volume | 798.85 Å3 |
| Hydrophobicity | 0.137 |
| Hydrophilicity | 1.377 |
| Buriedness | 0.749 |
| Don/acc character | 1.031 |
| SiteScore | 1.034 |
| D Score | 0.940 |
| Kd | — |
| Compound | GET |
| Residue | . / 3812 |
| Chain | WZ / 1 |
| Non-redundant | True |
| Interacting RNA chains | JA/1 |
| RNA environment detailled | protein |
| RNA environment global | RNA/Protein |
| RNA family chains | JA/1: rRNA |
| RNA family global | rRNA |
| Volume | 93.30 Å3 |
| Hydrophobicity | 0.000 |
| Hydrophilicity | 1.158 |
| Buriedness | 0.638 |
| Don/acc character | 1.687 |
| SiteScore | 0.501 |
| D Score | 0.357 |
| Kd | — |
| Compound | GET |
| Residue | . / 3813 |
| Chain | XZ / 1 |
| Non-redundant | True |
| Interacting RNA chains | JA/1 |
| RNA environment detailled | protein, ion, other |
| RNA environment global | RNA/Other |
| RNA family chains | JA/1: rRNA |
| RNA family global | rRNA |
| Volume | 474.37 Å3 |
| Hydrophobicity | 0.404 |
| Hydrophilicity | 1.021 |
| Buriedness | 0.773 |
| Don/acc character | 2.215 |
| SiteScore | 0.868 |
| D Score | 0.646 |
| Kd | — |
| Compound | GET |
| Residue | . / 2013 |
| Chain | CHA / 6 |
| Non-redundant | True |
| Interacting RNA chains | BC/6 |
| RNA environment detailled | protein |
| RNA environment global | RNA/Protein |
| RNA family chains | BC/6: rRNA |
| RNA family global | rRNA |
| Volume | 105.64 Å3 |
| Hydrophobicity | 0.233 |
| Hydrophilicity | 0.937 |
| Buriedness | 0.569 |
| Don/acc character | 1.616 |
| SiteScore | 0.885 |
| D Score | 0.720 |
| Kd | — |
| Compound | GET |
| Residue | . / 2014 |
| Chain | DHA / 6 |
| Non-redundant | True |
| Interacting RNA chains | BC/6 |
| RNA environment detailled | RNA-only |
| RNA environment global | RNA |
| RNA family chains | BC/6: rRNA |
| RNA family global | rRNA |
| Volume | 162.24 Å3 |
| Hydrophobicity | 0.071 |
| Hydrophilicity | 1.294 |
| Buriedness | 0.716 |
| Don/acc character | 1.364 |
| SiteScore | 0.765 |
| D Score | 0.439 |
| Kd | — |
| Compound | GET |
| Residue | . / 2015 |
| Chain | EHA / 6 |
| Non-redundant | True |
| Interacting RNA chains | BC/6 |
| RNA environment detailled | protein, ion |
| RNA environment global | RNA/Protein |
| RNA family chains | BC/6: rRNA |
| RNA family global | rRNA |
| Volume | 237.36 Å3 |
| Hydrophobicity | 0.063 |
| Hydrophilicity | 1.175 |
| Buriedness | 0.709 |
| Don/acc character | 1.500 |
| SiteScore | 0.900 |
| D Score | 0.652 |
| Kd | — |
| Compound | GET |
| Residue | . / 3844 |
| Chain | QYA / 5 |
| Non-redundant | True |
| Interacting RNA chains | KD/5 |
| RNA environment detailled | protein, ion |
| RNA environment global | RNA/Protein |
| RNA family chains | KD/5: rRNA |
| RNA family global | rRNA |
| Volume | 308.36 Å3 |
| Hydrophobicity | 0.018 |
| Hydrophilicity | 1.026 |
| Buriedness | 0.705 |
| Don/acc character | 4.950 |
| SiteScore | 0.973 |
| D Score | 0.792 |
| Kd | — |
| Compound | GET |
| Residue | . / 3845 |
| Chain | RYA / 5 |
| Non-redundant | True |
| Interacting RNA chains | KD/5 |
| RNA environment detailled | protein |
| RNA environment global | RNA/Protein |
| RNA family chains | KD/5: rRNA |
| RNA family global | rRNA |
| Volume | 391.71 Å3 |
| Hydrophobicity | 0.185 |
| Hydrophilicity | 1.208 |
| Buriedness | 0.771 |
| Don/acc character | 1.047 |
| SiteScore | 0.643 |
| D Score | 0.489 |
| Kd | — |
| Compound | GET |
| Residue | . / 3846 |
| Chain | SYA / 5 |
| Non-redundant | True |
| Interacting RNA chains | KD/5 |
| RNA environment detailled | protein |
| RNA environment global | RNA/Protein |
| RNA family chains | KD/5: rRNA |
| RNA family global | rRNA |
| Volume | 198.94 Å3 |
| Hydrophobicity | 0.544 |
| Hydrophilicity | 0.959 |
| Buriedness | 0.770 |
| Don/acc character | 1.766 |
| SiteScore | 0.595 |
| D Score | 0.488 |
| Kd | — |
| Compound | GET |
| Residue | . / 3847 |
| Chain | TYA / 5 |
| Non-redundant | True |
| Interacting RNA chains | KD/5 |
| RNA environment detailled | ion, other |
| RNA environment global | RNA/Other |
| RNA family chains | KD/5: rRNA |
| RNA family global | rRNA |
| Volume | 278.52 Å3 |
| Hydrophobicity | 0.056 |
| Hydrophilicity | 2.014 |
| Buriedness | 0.825 |
| Don/acc character | 1.078 |
| SiteScore | 1.065 |
| D Score | 0.561 |
| Kd | — |
| Compound | GET |
| Residue | . / 3848 |
| Chain | UYA / 5 |
| Non-redundant | True |
| Interacting RNA chains | KD/5 |
| RNA environment detailled | protein |
| RNA environment global | RNA/Protein |
| RNA family chains | KD/5: rRNA |
| RNA family global | rRNA |
| Volume | 301.84 Å3 |
| Hydrophobicity | 0.144 |
| Hydrophilicity | 1.233 |
| Buriedness | 0.771 |
| Don/acc character | 0.927 |
| SiteScore | 0.774 |
| D Score | 0.648 |
| Kd | — |
| Compound | GET |
| Residue | . / 3849 |
| Chain | VYA / 5 |
| Non-redundant | True |
| Interacting RNA chains | KD/5 |
| RNA environment detailled | protein, ion, other |
| RNA environment global | RNA/Other |
| RNA family chains | KD/5: rRNA |
| RNA family global | rRNA |
| Volume | 309.39 Å3 |
| Hydrophobicity | 0.014 |
| Hydrophilicity | 2.175 |
| Buriedness | 0.826 |
| Don/acc character | 0.936 |
| SiteScore | 0.798 |
| D Score | 0.247 |
| Kd | — |
| Compound | GET |
| Residue | . / 3850 |
| Chain | WYA / 5 |
| Non-redundant | True |
| Interacting RNA chains | MD/8, KD/5 |
| RNA environment detailled | protein, ion |
| RNA environment global | RNA/Protein |
| RNA family chains | KD/5: rRNA, MD/8: rRNA |
| RNA family global | rRNA |
| Volume | 501.47 Å3 |
| Hydrophobicity | 0.264 |
| Hydrophilicity | 1.396 |
| Buriedness | 0.740 |
| Don/acc character | 1.263 |
| SiteScore | 1.136 |
| D Score | 0.875 |
| Kd | — |
| Compound | GET |
| Residue | . / 3851 |
| Chain | XYA / 5 |
| Non-redundant | True |
| Interacting RNA chains | KD/5 |
| RNA environment detailled | ion |
| RNA environment global | RNA |
| RNA family chains | KD/5: rRNA |
| RNA family global | rRNA |
| Volume | 214.72 Å3 |
| Hydrophobicity | 0.045 |
| Hydrophilicity | 0.898 |
| Buriedness | 0.628 |
| Don/acc character | 4.884 |
| SiteScore | 0.819 |
| D Score | 0.624 |
| Kd | — |
| Compound | GET |
| Residue | . / 201 |
| Chain | TAB / n6 |
| Non-redundant | True |
| Interacting RNA chains | KD/5 |
| RNA environment detailled | protein, ion |
| RNA environment global | RNA/Protein |
| RNA family chains | KD/5: rRNA |
| RNA family global | rRNA |
| Volume | 240.79 Å3 |
| Hydrophobicity | 0.363 |
| Hydrophilicity | 0.934 |
| Buriedness | 0.730 |
| Don/acc character | 1.582 |
| SiteScore | 0.917 |
| D Score | 0.721 |
| Kd | — |