HARIBOSS

Harnessing RIBOnucleic acid - Small molecules Structures

Complex 8ev6

System information

Experimental technique X-ray
Experimental resolution 2.95
System mass 4563.75 kDa
Deposition year 2022
Molecule type RNA/Protein
# RNA entities 6
Organism Thermus
RCSB PDB Entry 8ev6
Reference Seely Savannah M., Parajuli Narayan P., De Tarafder Arindam, Ge Xueliang, Sanyal Suparna, Gagnon Matthieu G.. . Molecular basis of the pleiotropic effects by the antibiotic amikacin on the ribosome Nature Communications

Compound AKN
Residue . / 3936
Chain HNA / 1A
Non-redundant True
Interacting RNA chains CB/1x, A/1A
Volume 617.06 Å3
Hydrophobicity 0.280
Hydrophilicity 0.916
Buriedness 0.706
Don/acc character 1.826
SiteScore 1.029
D Score 1.065

Compound AKN
Residue . / 1913
Chain BDB / 1a
Non-redundant True
Interacting RNA chains FA/1a
Volume 602.65 Å3
Hydrophobicity 0.056
Hydrophilicity 1.096
Buriedness 0.697
Don/acc character 2.765
SiteScore 0.999
D Score 1.001

Compound AKN
Residue . / 3576
Chain BBC / 2A
Non-redundant True
Interacting RNA chains EB/2A, GD/2x
Volume 702.12 Å3
Hydrophobicity 0.185
Hydrophilicity 0.977
Buriedness 0.706
Don/acc character 1.862
SiteScore 1.018
D Score 1.045

Compound AKN
Residue . / 1911
Chain XOC / 2a
Non-redundant False
Interacting RNA chains JC/2a
Volume 263.42 Å3
Hydrophobicity 0.083
Hydrophilicity 0.962
Buriedness 0.675
Don/acc character 3.045
SiteScore 0.875
D Score 0.872