Complex 5ndv
System information
| Experimental technique | X-ray |
| Experimental resolution | 3.30 |
| System mass | 6227.43 kDa |
| Deposition year | 2017 |
| Molecule type | RNA/Protein |
| # RNA entities | 3 |
| Organism | Saccharomyces |
| RCSB PDB Entry | 5ndv |
| 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 |
| Compound | PAR |
| Residue | . / 3401 |
| Chain | AF / 1 |
| Non-redundant | True |
| Interacting RNA chains | A/1 |
| Volume | 214.03 Å3 |
| Hydrophobicity | 0.078 |
| Hydrophilicity | 1.271 |
| Buriedness | 0.723 |
| Don/acc character | 3.253 |
| SiteScore | 0.847 |
| D Score | 0.741 |
| Compound | PAR |
| Residue | . / 3406 |
| Chain | FF / 1 |
| Non-redundant | True |
| Interacting RNA chains | A/1 |
| Volume | 256.91 Å3 |
| Hydrophobicity | 0.031 |
| Hydrophilicity | 1.170 |
| Buriedness | 0.655 |
| Don/acc character | 1.973 |
| SiteScore | 0.847 |
| D Score | 0.792 |
| Compound | PAR |
| Residue | . / 3423 |
| Chain | WF / 1 |
| Non-redundant | True |
| Interacting RNA chains | A/1 |
| Volume | 915.47 Å3 |
| Hydrophobicity | 0.075 |
| Hydrophilicity | 1.177 |
| Buriedness | 0.709 |
| Don/acc character | 1.504 |
| SiteScore | 1.007 |
| D Score | 0.982 |
| Compound | PAR |
| Residue | . / 3432 |
| Chain | FG / 1 |
| Non-redundant | True |
| Interacting RNA chains | A/1 |
| Volume | 300.81 Å3 |
| Hydrophobicity | 0.144 |
| Hydrophilicity | 1.075 |
| Buriedness | 0.640 |
| Don/acc character | 5.919 |
| SiteScore | 0.892 |
| D Score | 0.885 |
| Compound | PAR |
| Residue | . / 3434 |
| Chain | HG / 1 |
| Non-redundant | True |
| Interacting RNA chains | A/1 |
| Volume | 446.59 Å3 |
| Hydrophobicity | 0.081 |
| Hydrophilicity | 1.122 |
| Buriedness | 0.661 |
| Don/acc character | 1.839 |
| SiteScore | 0.975 |
| D Score | 0.970 |
| Compound | PAR |
| Residue | . / 202 |
| Chain | MKA / 4 |
| Non-redundant | True |
| Interacting RNA chains | C/4 |
| Volume | 216.78 Å3 |
| Hydrophobicity | 0.018 |
| Hydrophilicity | 1.249 |
| Buriedness | 0.666 |
| Don/acc character | 1.770 |
| SiteScore | 0.789 |
| D Score | 0.690 |
| Compound | PAR |
| Residue | . / 1901 |
| Chain | VPA / 2 |
| Non-redundant | True |
| Interacting RNA chains | SA/2 |
| Volume | 346.43 Å3 |
| Hydrophobicity | 0.114 |
| Hydrophilicity | 1.453 |
| Buriedness | 0.711 |
| Don/acc character | 2.295 |
| SiteScore | 1.009 |
| D Score | 0.893 |
| Compound | PAR |
| Residue | . / 3402 |
| Chain | TYA / 5 |
| Non-redundant | True |
| Interacting RNA chains | AC/5 |
| Volume | 393.08 Å3 |
| Hydrophobicity | 0.065 |
| Hydrophilicity | 1.108 |
| Buriedness | 0.663 |
| Don/acc character | 1.813 |
| SiteScore | 0.977 |
| D Score | 0.977 |
| Compound | PAR |
| Residue | . / 3405 |
| Chain | WYA / 5 |
| Non-redundant | True |
| Interacting RNA chains | AC/5 |
| Volume | 250.05 Å3 |
| Hydrophobicity | 0.043 |
| Hydrophilicity | 1.329 |
| Buriedness | 0.718 |
| Don/acc character | 3.558 |
| SiteScore | 0.848 |
| D Score | 0.725 |
| Compound | PAR |
| Residue | . / 3419 |
| Chain | KZA / 5 |
| Non-redundant | True |
| Interacting RNA chains | AC/5 |
| Volume | 429.78 Å3 |
| Hydrophobicity | 0.084 |
| Hydrophilicity | 1.182 |
| Buriedness | 0.707 |
| Don/acc character | 1.990 |
| SiteScore | 0.964 |
| D Score | 0.925 |
| Compound | PAR |
| Residue | . / 3426 |
| Chain | RZA / 5 |
| Non-redundant | True |
| Interacting RNA chains | AC/5 |
| Volume | 241.13 Å3 |
| Hydrophobicity | 0.034 |
| Hydrophilicity | 1.256 |
| Buriedness | 0.668 |
| Don/acc character | 3.788 |
| SiteScore | 0.860 |
| D Score | 0.778 |
| Compound | PAR |
| Residue | . / 3428 |
| Chain | TZA / 5 |
| Non-redundant | True |
| Interacting RNA chains | AC/5 |
| Volume | - |
| Hydrophobicity | - |
| Hydrophilicity | - |
| Buriedness | - |
| Don/acc character | - |
| SiteScore | - |
| D Score | - |
| Compound | PAR |
| Residue | . / 1903 |
| Chain | TFC / 6 |
| Non-redundant | True |
| Interacting RNA chains | SD/6 |
| Volume | 1191.92 Å3 |
| Hydrophobicity | 0.107 |
| Hydrophilicity | 1.247 |
| Buriedness | 0.724 |
| Don/acc character | 2.239 |
| SiteScore | 1.017 |
| D Score | 0.968 |