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 |