HARIBOSS

Harnessing RIBOnucleic acid - Small molecules Structures

Complex 5ndg

System information

Experimental technique X-ray
Experimental resolution 3.70
System mass 6233.17 kDa
Deposition year 2017
Molecule type RNA/Protein
# RNA entities 3
Organism Saccharomyces
RCSB PDB Entry 5ndg
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 GET
Residue . / 2012
Chain KJ / 2
Non-redundant True
Interacting RNA chains A/2
Volume -
Hydrophobicity -
Hydrophilicity -
Buriedness -
Don/acc character -
SiteScore -
D Score -

Compound GET
Residue . / 3810
Chain UZ / 1
Non-redundant True
Interacting RNA chains LA/4, JA/1
Volume 686.34 Å3
Hydrophobicity 0.166
Hydrophilicity 0.997
Buriedness 0.687
Don/acc character 2.585
SiteScore 1.001
D Score 1.027

Compound GET
Residue . / 2014
Chain DHA / 6
Non-redundant True
Interacting RNA chains BC/6
Volume 140.97 Å3
Hydrophobicity 0.050
Hydrophilicity 1.229
Buriedness 0.695
Don/acc character 1.424
SiteScore 0.567
D Score 0.404

Compound GET
Residue . / 3851
Chain XYA / 5
Non-redundant True
Interacting RNA chains KD/5
Volume 179.73 Å3
Hydrophobicity 0.016
Hydrophilicity 0.913
Buriedness 0.609
Don/acc character 3.662
SiteScore 0.647
D Score 0.600