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 | 5 |
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 |
Compound | 8UZ |
Residue | . / 2201 |
Chain | ED / 13 |
Non-redundant | False |
Interacting RNA chains | A/13 |
Volume | 298.41 Å3 |
Hydrophobicity | 0.139 |
Hydrophilicity | 1.156 |
Buriedness | 0.693 |
Don/acc character | 2.262 |
SiteScore | 0.959 |
D Score | 0.931 |
Compound | 8UZ |
Residue | . / 2201 |
Chain | DL / 1G |
Non-redundant | False |
Interacting RNA chains | J/1G |
Volume | 239.76 Å3 |
Hydrophobicity | 0.089 |
Hydrophilicity | 1.269 |
Buriedness | 0.698 |
Don/acc character | 2.148 |
SiteScore | 0.885 |
D Score | 0.797 |
Compound | 8UZ |
Residue | . / 3002 |
Chain | WS / 1H |
Non-redundant | False |
Interacting RNA chains | T/1H |
Volume | - |
Hydrophobicity | - |
Hydrophilicity | - |
Buriedness | - |
Don/acc character | - |
SiteScore | - |
D Score | - |
Compound | 8UZ |
Residue | . / 3003 |
Chain | XS / 1H |
Non-redundant | False |
Interacting RNA chains | T/1H |
Volume | 196.88 Å3 |
Hydrophobicity | 0.025 |
Hydrophilicity | 1.416 |
Buriedness | 0.741 |
Don/acc character | 2.078 |
SiteScore | 0.717 |
D Score | 0.523 |
Compound | 8UZ |
Residue | . / 3004 |
Chain | YS / 1H |
Non-redundant | False |
Interacting RNA chains | T/1H |
Volume | 104.96 Å3 |
Hydrophobicity | 0.015 |
Hydrophilicity | 1.011 |
Buriedness | 0.646 |
Don/acc character | 2.570 |
SiteScore | 0.566 |
D Score | 0.479 |
Compound | 8UZ |
Residue | . / 3005 |
Chain | ZS / 1H |
Non-redundant | True |
Interacting RNA chains | T/1H |
Volume | 176.64 Å3 |
Hydrophobicity | 0.033 |
Hydrophilicity | 1.180 |
Buriedness | 0.567 |
Don/acc character | 2.041 |
SiteScore | 0.909 |
D Score | 0.891 |
Compound | 8UZ |
Residue | . / 3002 |
Chain | PSA / 14 |
Non-redundant | True |
Interacting RNA chains | EA/14 |
Volume | - |
Hydrophobicity | - |
Hydrophilicity | - |
Buriedness | - |
Don/acc character | - |
SiteScore | - |
D Score | - |
Compound | 8UZ |
Residue | . / 3003 |
Chain | QSA / 14 |
Non-redundant | True |
Interacting RNA chains | EA/14 |
Volume | 215.40 Å3 |
Hydrophobicity | 0.124 |
Hydrophilicity | 1.243 |
Buriedness | 0.711 |
Don/acc character | 1.464 |
SiteScore | 0.715 |
D Score | 0.585 |
Compound | 8UZ |
Residue | . / 3004 |
Chain | RSA / 14 |
Non-redundant | True |
Interacting RNA chains | EA/14 |
Volume | 75.12 Å3 |
Hydrophobicity | 0.110 |
Hydrophilicity | 0.945 |
Buriedness | 0.631 |
Don/acc character | 5.003 |
SiteScore | 0.584 |
D Score | 0.511 |
Compound | 8UZ |
Residue | . / 3005 |
Chain | SSA / 14 |
Non-redundant | False |
Interacting RNA chains | EA/14 |
Volume | 180.42 Å3 |
Hydrophobicity | 0.037 |
Hydrophilicity | 1.215 |
Buriedness | 0.589 |
Don/acc character | 1.976 |
SiteScore | 0.885 |
D Score | 0.844 |