Complex 5ndw
System information
| Experimental technique | X-ray |
| Experimental resolution | 3.70 |
| System mass | 6188.11 kDa |
| Deposition year | 2017 |
| Molecule type | RNA/Protein |
| # RNA entities | 1 |
| Organism | Saccharomyces |
| RCSB PDB Entry | 5ndw |
| 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,
NR_all_18586.78
BGSU version: 4.48 |
| Compound | 8UZ |
| Residue | . / 3886 |
| Chain | TX / 1 |
| Non-redundant | True |
| Interacting RNA chains | A/1 |
| RNA environment detailled | protein |
| RNA environment global | RNA/Protein |
| RNA family chains | A/1: rRNA |
| RNA family global | rRNA |
| Volume | 465.11 Å3 |
| Hydrophobicity | 0.115 |
| Hydrophilicity | 1.632 |
| Buriedness | 0.725 |
| Don/acc character | 1.371 |
| SiteScore | 1.018 |
| D Score | 0.843 |
| Kd | — |
| Compound | 8UZ |
| Residue | . / 3887 |
| Chain | UX / 1 |
| Non-redundant | True |
| Interacting RNA chains | A/1 |
| RNA environment detailled | RNA-only |
| RNA environment global | RNA |
| RNA family chains | A/1: rRNA |
| RNA family global | rRNA |
| Volume | 159.50 Å3 |
| Hydrophobicity | 0.094 |
| Hydrophilicity | 0.962 |
| Buriedness | 0.663 |
| Don/acc character | 1.989 |
| SiteScore | 0.720 |
| D Score | 0.483 |
| Kd | — |
| Compound | 8UZ |
| Residue | . / 3888 |
| Chain | VX / 1 |
| Non-redundant | True |
| Interacting RNA chains | A/1 |
| RNA environment detailled | RNA-only |
| RNA environment global | RNA |
| RNA family chains | A/1: rRNA |
| RNA family global | rRNA |
| Volume | 53.17 Å3 |
| Hydrophobicity | 0.012 |
| Hydrophilicity | 0.954 |
| Buriedness | 0.613 |
| Don/acc character | 1.087 |
| SiteScore | 0.661 |
| D Score | 0.421 |
| Kd | — |
| Compound | 8UZ |
| Residue | . / 3889 |
| Chain | WX / 1 |
| Non-redundant | True |
| Interacting RNA chains | A/1 |
| RNA environment detailled | RNA-only |
| RNA environment global | RNA |
| RNA family chains | A/1: rRNA |
| RNA family global | rRNA |
| Volume | 128.63 Å3 |
| Hydrophobicity | 0.813 |
| Hydrophilicity | 0.996 |
| Buriedness | 0.742 |
| Don/acc character | 0.925 |
| SiteScore | 0.907 |
| D Score | 0.700 |
| Kd | — |
| Compound | 8UZ |
| Residue | . / 3890 |
| Chain | XX / 1 |
| Non-redundant | True |
| Interacting RNA chains | B/2, A/1 |
| RNA environment detailled | protein |
| RNA environment global | RNA/Protein |
| RNA family chains | A/1: rRNA, B/2: rRNA |
| RNA family global | rRNA |
| Volume | 311.10 Å3 |
| Hydrophobicity | 0.190 |
| Hydrophilicity | 1.158 |
| Buriedness | 0.753 |
| Don/acc character | 2.254 |
| SiteScore | 0.988 |
| D Score | 0.759 |
| Kd | — |
| Compound | 8UZ |
| Residue | . / 3891 |
| Chain | YX / 1 |
| Non-redundant | True |
| Interacting RNA chains | A/1 |
| RNA environment detailled | protein |
| RNA environment global | RNA/Protein |
| RNA family chains | A/1: rRNA |
| RNA family global | rRNA |
| Volume | 263.77 Å3 |
| Hydrophobicity | 0.033 |
| Hydrophilicity | 1.029 |
| Buriedness | 0.711 |
| Don/acc character | 1.987 |
| SiteScore | 0.946 |
| D Score | 0.756 |
| Kd | — |
| Compound | 8UZ |
| Residue | . / 3892 |
| Chain | ZX / 1 |
| Non-redundant | True |
| Interacting RNA chains | A/1 |
| RNA environment detailled | protein |
| RNA environment global | RNA/Protein |
| RNA family chains | A/1: rRNA |
| RNA family global | rRNA |
| Volume | 103.24 Å3 |
| Hydrophobicity | 0.393 |
| Hydrophilicity | 0.770 |
| Buriedness | 0.680 |
| Don/acc character | 1.281 |
| SiteScore | 0.609 |
| D Score | 0.544 |
| Kd | — |
| Compound | 8UZ |
| Residue | . / 3893 |
| Chain | AY / 1 |
| Non-redundant | True |
| Interacting RNA chains | A/1 |
| RNA environment detailled | ion |
| RNA environment global | RNA |
| RNA family chains | A/1: rRNA |
| RNA family global | rRNA |
| Volume | 393.76 Å3 |
| Hydrophobicity | 0.057 |
| Hydrophilicity | 1.839 |
| Buriedness | 0.719 |
| Don/acc character | 2.208 |
| SiteScore | 1.164 |
| D Score | 0.772 |
| Kd | — |
| Compound | 8UZ |
| Residue | . / 3894 |
| Chain | BY / 1 |
| Non-redundant | True |
| Interacting RNA chains | A/1 |
| RNA environment detailled | RNA-only |
| RNA environment global | RNA |
| RNA family chains | A/1: rRNA |
| RNA family global | rRNA |
| Volume | 695.60 Å3 |
| Hydrophobicity | 0.112 |
| Hydrophilicity | 1.107 |
| Buriedness | 0.720 |
| Don/acc character | 1.549 |
| SiteScore | 1.165 |
| D Score | 1.011 |
| Kd | — |
| Compound | 8UZ |
| Residue | . / 3895 |
| Chain | CY / 1 |
| Non-redundant | True |
| Interacting RNA chains | A/1 |
| RNA environment detailled | protein |
| RNA environment global | RNA/Protein |
| RNA family chains | A/1: rRNA |
| RNA family global | rRNA |
| Volume | 253.48 Å3 |
| Hydrophobicity | 0.045 |
| Hydrophilicity | 1.129 |
| Buriedness | 0.635 |
| Don/acc character | 2.214 |
| SiteScore | 0.722 |
| D Score | 0.650 |
| Kd | — |
| Compound | 8UZ |
| Residue | . / 2029 |
| Chain | BDA / 2 |
| Non-redundant | True |
| Interacting RNA chains | B/2 |
| RNA environment detailled | ion |
| RNA environment global | RNA |
| RNA family chains | B/2: rRNA |
| RNA family global | rRNA |
| Volume | 539.20 Å3 |
| Hydrophobicity | 0.184 |
| Hydrophilicity | 1.073 |
| Buriedness | 0.739 |
| Don/acc character | 1.672 |
| SiteScore | 1.177 |
| D Score | 1.034 |
| Kd | — |
| Compound | 8UZ |
| Residue | . / 2030 |
| Chain | CDA / 2 |
| Non-redundant | True |
| Interacting RNA chains | B/2 |
| RNA environment detailled | protein |
| RNA environment global | RNA/Protein |
| RNA family chains | B/2: rRNA |
| RNA family global | rRNA |
| Volume | 633.18 Å3 |
| Hydrophobicity | 0.114 |
| Hydrophilicity | 1.173 |
| Buriedness | 0.731 |
| Don/acc character | 1.256 |
| SiteScore | 1.107 |
| D Score | 0.913 |
| Kd | — |
| Compound | 8UZ |
| Residue | . / 2031 |
| Chain | DDA / 2 |
| Non-redundant | True |
| Interacting RNA chains | B/2 |
| RNA environment detailled | RNA-only |
| RNA environment global | RNA |
| RNA family chains | B/2: rRNA |
| RNA family global | rRNA |
| Volume | 192.42 Å3 |
| Hydrophobicity | 0.150 |
| Hydrophilicity | 1.263 |
| Buriedness | 0.755 |
| Don/acc character | 1.113 |
| SiteScore | 0.766 |
| D Score | 0.440 |
| Kd | — |
| Compound | 8UZ |
| Residue | . / 214 |
| Chain | RDA / 3 |
| Non-redundant | True |
| Interacting RNA chains | C/3 |
| RNA environment detailled | protein, ion |
| RNA environment global | RNA/Protein |
| RNA family chains | C/3: rRNA |
| RNA family global | rRNA |
| Volume | 272.00 Å3 |
| Hydrophobicity | 0.102 |
| Hydrophilicity | 0.900 |
| Buriedness | 0.645 |
| Don/acc character | 2.155 |
| SiteScore | 0.782 |
| D Score | 0.765 |
| Kd | — |
| Compound | 8UZ |
| Residue | . / 220 |
| Chain | LEA / 4 |
| Non-redundant | True |
| Interacting RNA chains | D/4, A/1 |
| RNA environment detailled | ion |
| RNA environment global | RNA |
| RNA family chains | A/1: rRNA, D/4: rRNA |
| RNA family global | rRNA |
| Volume | 672.97 Å3 |
| Hydrophobicity | 0.081 |
| Hydrophilicity | 1.804 |
| Buriedness | 0.686 |
| Don/acc character | 0.498 |
| SiteScore | 0.992 |
| D Score | 0.763 |
| Kd | — |
| Compound | 8UZ |
| Residue | . / 3850 |
| Chain | TVA / 5 |
| Non-redundant | True |
| Interacting RNA chains | E/5 |
| RNA environment detailled | protein |
| RNA environment global | RNA/Protein |
| RNA family chains | E/5: rRNA |
| RNA family global | rRNA |
| Volume | 71.69 Å3 |
| Hydrophobicity | 0.280 |
| Hydrophilicity | 0.884 |
| Buriedness | 0.654 |
| Don/acc character | 0.631 |
| SiteScore | 0.579 |
| D Score | 0.503 |
| Kd | — |
| Compound | 8UZ |
| Residue | . / 3851 |
| Chain | UVA / 5 |
| Non-redundant | True |
| Interacting RNA chains | E/5 |
| RNA environment detailled | RNA-only |
| RNA environment global | RNA |
| RNA family chains | E/5: rRNA |
| RNA family global | rRNA |
| Volume | 262.05 Å3 |
| Hydrophobicity | 0.034 |
| Hydrophilicity | 1.117 |
| Buriedness | 0.669 |
| Don/acc character | 1.209 |
| SiteScore | 0.966 |
| D Score | 0.766 |
| Kd | — |
| Compound | 8UZ |
| Residue | . / 3852 |
| Chain | VVA / 5 |
| Non-redundant | True |
| Interacting RNA chains | E/5 |
| RNA environment detailled | protein, ion |
| RNA environment global | RNA/Protein |
| RNA family chains | E/5: rRNA |
| RNA family global | rRNA |
| Volume | 512.79 Å3 |
| Hydrophobicity | 0.137 |
| Hydrophilicity | 1.238 |
| Buriedness | 0.706 |
| Don/acc character | 1.324 |
| SiteScore | 1.005 |
| D Score | 0.960 |
| Kd | — |
| Compound | 8UZ |
| Residue | . / 3853 |
| Chain | WVA / 5 |
| Non-redundant | True |
| Interacting RNA chains | E/5 |
| RNA environment detailled | protein, ion |
| RNA environment global | RNA/Protein |
| RNA family chains | E/5: rRNA |
| RNA family global | rRNA |
| Volume | 265.83 Å3 |
| Hydrophobicity | 0.068 |
| Hydrophilicity | 0.820 |
| Buriedness | 0.701 |
| Don/acc character | 3.195 |
| SiteScore | 0.969 |
| D Score | 0.804 |
| Kd | — |
| Compound | 8UZ |
| Residue | . / 3854 |
| Chain | XVA / 5 |
| Non-redundant | True |
| Interacting RNA chains | E/5 |
| RNA environment detailled | protein |
| RNA environment global | RNA/Protein |
| RNA family chains | E/5: rRNA |
| RNA family global | rRNA |
| Volume | 306.64 Å3 |
| Hydrophobicity | 0.022 |
| Hydrophilicity | 1.410 |
| Buriedness | 0.746 |
| Don/acc character | 1.881 |
| SiteScore | 0.950 |
| D Score | 0.823 |
| Kd | — |
| Compound | 8UZ |
| Residue | . / 3855 |
| Chain | YVA / 5 |
| Non-redundant | True |
| Interacting RNA chains | E/5 |
| RNA environment detailled | RNA-only |
| RNA environment global | RNA |
| RNA family chains | E/5: rRNA |
| RNA family global | rRNA |
| Volume | 335.80 Å3 |
| Hydrophobicity | 0.024 |
| Hydrophilicity | 1.844 |
| Buriedness | 0.685 |
| Don/acc character | 0.718 |
| SiteScore | 1.119 |
| D Score | 0.721 |
| Kd | — |
| Compound | 8UZ |
| Residue | . / 3856 |
| Chain | ZVA / 5 |
| Non-redundant | True |
| Interacting RNA chains | E/5 |
| RNA environment detailled | protein |
| RNA environment global | RNA/Protein |
| RNA family chains | E/5: rRNA |
| RNA family global | rRNA |
| Volume | 307.67 Å3 |
| Hydrophobicity | 0.000 |
| Hydrophilicity | 1.788 |
| Buriedness | 0.721 |
| Don/acc character | 2.145 |
| SiteScore | 0.811 |
| D Score | 0.527 |
| Kd | — |
| Compound | 8UZ |
| Residue | . / 3857 |
| Chain | AWA / 5 |
| Non-redundant | True |
| Interacting RNA chains | E/5 |
| RNA environment detailled | RNA-only |
| RNA environment global | RNA |
| RNA family chains | E/5: rRNA |
| RNA family global | rRNA |
| Volume | 64.48 Å3 |
| Hydrophobicity | 0.129 |
| Hydrophilicity | 1.068 |
| Buriedness | 0.557 |
| Don/acc character | 1.671 |
| SiteScore | 0.744 |
| D Score | 0.526 |
| Kd | — |
| Compound | 8UZ |
| Residue | . / 2061 |
| Chain | FCB / 6 |
| Non-redundant | True |
| Interacting RNA chains | F/6 |
| RNA environment detailled | protein, ion |
| RNA environment global | RNA/Protein |
| RNA family chains | F/6: rRNA |
| RNA family global | rRNA |
| Volume | 776.90 Å3 |
| Hydrophobicity | 0.047 |
| Hydrophilicity | 1.369 |
| Buriedness | 0.770 |
| Don/acc character | 1.575 |
| SiteScore | 1.198 |
| D Score | 0.956 |
| Kd | — |
| Compound | 8UZ |
| Residue | . / 209 |
| Chain | OCB / 7 |
| Non-redundant | True |
| Interacting RNA chains | G/7 |
| RNA environment detailled | protein, ion |
| RNA environment global | RNA/Protein |
| RNA family chains | G/7: rRNA |
| RNA family global | rRNA |
| Volume | 249.70 Å3 |
| Hydrophobicity | 0.105 |
| Hydrophilicity | 0.971 |
| Buriedness | 0.652 |
| Don/acc character | 1.292 |
| SiteScore | 0.671 |
| D Score | 0.615 |
| Kd | — |