Complex 5ndj
System information
| Experimental technique | X-ray |
| Experimental resolution | 3.15 |
| System mass | 4529.17 kDa |
| Deposition year | 2017 |
| Molecule type | RNA/Protein |
| # RNA entities | 1 |
| Organism | Thermus |
| RCSB PDB Entry | 5ndj |
| 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_65795.87,
NR_all_97519.80
BGSU version: 4.48 |
| Compound | 8UZ |
| Residue | . / 2201 |
| Chain | ED / 13 |
| Non-redundant | True |
| Interacting RNA chains | A/13 |
| RNA environment detailled | RNA-only |
| RNA environment global | RNA |
| RNA family chains | A/13: rRNA |
| RNA family global | rRNA |
| Volume | 302.87 Å3 |
| Hydrophobicity | 0.124 |
| Hydrophilicity | 1.085 |
| Buriedness | 0.692 |
| Don/acc character | 2.223 |
| SiteScore | 1.052 |
| D Score | 0.881 |
| Kd | — |
| Compound | 8UZ |
| Residue | . / 2202 |
| Chain | FD / 13 |
| Non-redundant | True |
| Interacting RNA chains | A/13 |
| RNA environment detailled | protein, ion |
| RNA environment global | RNA/Protein |
| RNA family chains | A/13: rRNA |
| RNA family global | rRNA |
| Volume | 114.56 Å3 |
| Hydrophobicity | 0.079 |
| Hydrophilicity | 1.175 |
| Buriedness | 0.729 |
| Don/acc character | 1.765 |
| SiteScore | 0.842 |
| D Score | 0.578 |
| Kd | — |
| Compound | 8UZ |
| Residue | . / 2201 |
| Chain | DL / 1G |
| Non-redundant | True |
| Interacting RNA chains | J/1G |
| RNA environment detailled | RNA-only |
| RNA environment global | RNA |
| RNA family chains | J/1G: rRNA |
| RNA family global | rRNA |
| Volume | 242.50 Å3 |
| Hydrophobicity | 0.052 |
| Hydrophilicity | 1.231 |
| Buriedness | 0.698 |
| Don/acc character | 1.980 |
| SiteScore | 0.985 |
| D Score | 0.746 |
| Kd | — |
| Compound | 8UZ |
| Residue | . / 2202 |
| Chain | EL / 1G |
| Non-redundant | True |
| Interacting RNA chains | J/1G |
| RNA environment detailled | protein, ion |
| RNA environment global | RNA/Protein |
| RNA family chains | J/1G: rRNA |
| RNA family global | rRNA |
| Volume | 193.11 Å3 |
| Hydrophobicity | 0.112 |
| Hydrophilicity | 1.100 |
| Buriedness | 0.697 |
| Don/acc character | 2.708 |
| SiteScore | 0.891 |
| D Score | 0.608 |
| Kd | — |
| Compound | 8UZ |
| Residue | . / 3002 |
| Chain | WS / 1H |
| Non-redundant | True |
| Interacting RNA chains | T/1H |
| RNA environment detailled | RNA-only |
| RNA environment global | RNA |
| RNA family chains | T/1H: rRNA |
| RNA family global | rRNA |
| Volume | 99.47 Å3 |
| Hydrophobicity | 0.008 |
| Hydrophilicity | 0.650 |
| Buriedness | 0.439 |
| Don/acc character | 4.483 |
| SiteScore | 1.052 |
| D Score | 0.991 |
| Kd | — |
| Compound | 8UZ |
| Residue | . / 3003 |
| Chain | XS / 1H |
| Non-redundant | True |
| Interacting RNA chains | T/1H |
| RNA environment detailled | RNA-only |
| RNA environment global | RNA |
| RNA family chains | T/1H: rRNA |
| RNA family global | rRNA |
| Volume | 209.92 Å3 |
| Hydrophobicity | 0.000 |
| Hydrophilicity | 1.438 |
| Buriedness | 0.790 |
| Don/acc character | 2.125 |
| SiteScore | 0.912 |
| D Score | 0.562 |
| Kd | — |
| Compound | 8UZ |
| Residue | . / 3004 |
| Chain | YS / 1H |
| Non-redundant | True |
| Interacting RNA chains | T/1H |
| RNA environment detailled | RNA-only |
| RNA environment global | RNA |
| RNA family chains | T/1H: rRNA |
| RNA family global | rRNA |
| Volume | 146.12 Å3 |
| Hydrophobicity | 0.026 |
| Hydrophilicity | 1.024 |
| Buriedness | 0.676 |
| Don/acc character | 3.217 |
| SiteScore | 0.749 |
| D Score | 0.513 |
| Kd | — |
| Compound | 8UZ |
| Residue | . / 3005 |
| Chain | ZS / 1H |
| Non-redundant | True |
| Interacting RNA chains | T/1H |
| RNA environment detailled | RNA-only |
| RNA environment global | RNA |
| RNA family chains | T/1H: rRNA |
| RNA family global | rRNA |
| Volume | 186.59 Å3 |
| Hydrophobicity | 0.005 |
| Hydrophilicity | 1.224 |
| Buriedness | 0.569 |
| Don/acc character | 2.207 |
| SiteScore | 1.063 |
| D Score | 0.882 |
| Kd | — |
| Compound | 8UZ |
| Residue | . / 3002 |
| Chain | PSA / 14 |
| Non-redundant | True |
| Interacting RNA chains | EA/14 |
| RNA environment detailled | RNA-only |
| RNA environment global | RNA |
| RNA family chains | EA/14: rRNA |
| RNA family global | rRNA |
| Volume | 105.99 Å3 |
| Hydrophobicity | 0.006 |
| Hydrophilicity | 0.650 |
| Buriedness | 0.463 |
| Don/acc character | 4.166 |
| SiteScore | 1.068 |
| D Score | 1.006 |
| Kd | — |
| Compound | 8UZ |
| Residue | . / 3003 |
| Chain | QSA / 14 |
| Non-redundant | True |
| Interacting RNA chains | EA/14 |
| RNA environment detailled | RNA-only |
| RNA environment global | RNA |
| RNA family chains | EA/14: rRNA |
| RNA family global | rRNA |
| Volume | 222.26 Å3 |
| Hydrophobicity | 0.006 |
| Hydrophilicity | 1.382 |
| Buriedness | 0.743 |
| Don/acc character | 1.670 |
| SiteScore | 0.938 |
| D Score | 0.626 |
| Kd | — |
| Compound | 8UZ |
| Residue | . / 3004 |
| Chain | RSA / 14 |
| Non-redundant | True |
| Interacting RNA chains | EA/14 |
| RNA environment detailled | RNA-only |
| RNA environment global | RNA |
| RNA family chains | EA/14: rRNA |
| RNA family global | rRNA |
| Volume | 134.46 Å3 |
| Hydrophobicity | 0.132 |
| Hydrophilicity | 0.908 |
| Buriedness | 0.694 |
| Don/acc character | 2.142 |
| SiteScore | 0.814 |
| D Score | 0.600 |
| Kd | — |
| Compound | 8UZ |
| Residue | . / 3005 |
| Chain | SSA / 14 |
| Non-redundant | True |
| Interacting RNA chains | EA/14 |
| RNA environment detailled | RNA-only |
| RNA environment global | RNA |
| RNA family chains | EA/14: rRNA |
| RNA family global | rRNA |
| Volume | 183.16 Å3 |
| Hydrophobicity | 0.016 |
| Hydrophilicity | 1.244 |
| Buriedness | 0.595 |
| Don/acc character | 2.509 |
| SiteScore | 1.012 |
| D Score | 0.803 |
| Kd | — |
| Compound | 8UZ |
| Residue | . / 3006 |
| Chain | TSA / 14 |
| Non-redundant | True |
| Interacting RNA chains | EA/14, J/1G |
| RNA environment detailled | protein |
| RNA environment global | RNA/Protein |
| RNA family chains | J/1G: rRNA, EA/14: rRNA |
| RNA family global | rRNA |
| Volume | 335.11 Å3 |
| Hydrophobicity | 0.169 |
| Hydrophilicity | 1.060 |
| Buriedness | 0.654 |
| Don/acc character | 1.589 |
| SiteScore | 0.971 |
| D Score | 0.987 |
| Kd | — |