HARIBOSS

Harnessing RIBOnucleic acid - Small molecules Structures

Complex 8ifc

System information

Experimental technique Electron Microscopy
Experimental resolution 2.90
System mass 2212.46 kDa
Deposition year 2023
Molecule type RNA/Protein
# RNA entities 6
Organism Escherichia
RCSB PDB Entry 8ifc
Reference Tomono Junta, Asano Kosuke, Chiashi Takuma, Suzuki Masato, Igarashi Masayuki, Takahashi Yoshiaki, Tanaka Yoshikazu, Yokoyama Takeshi. . Direct visualization of ribosomes in the cell-free system revealed the functional evolution of aminoglycoside The Journal of Biochemistry

Compound 84G
Residue . / 1791
Chain LI / A
Non-redundant True
Interacting RNA chains CB/7, A/A
Volume 344.03 Å3
Hydrophobicity 0.122
Hydrophilicity 1.091
Buriedness 0.656
Don/acc character 2.127
SiteScore 0.802
D Score 0.760

Compound 84G
Residue . / 1792
Chain MI / A
Non-redundant True
Interacting RNA chains A/A
Volume 873.28 Å3
Hydrophobicity 0.160
Hydrophilicity 1.180
Buriedness 0.716
Don/acc character 1.729
SiteScore 1.012
D Score 0.985

Compound 84G
Residue . / 1793
Chain NI / A
Non-redundant False
Interacting RNA chains A/A
Volume 899.35 Å3
Hydrophobicity 0.092
Hydrophilicity 1.255
Buriedness 0.730
Don/acc character 2.059
SiteScore 1.021
D Score 0.969

Compound 84G
Residue . / 6249
Chain US / a
Non-redundant True
Interacting RNA chains V/a, BB/6
Volume 668.16 Å3
Hydrophobicity 0.046
Hydrophilicity 1.067
Buriedness 0.679
Don/acc character 1.644
SiteScore 0.987
D Score 1.000

Compound 84G
Residue . / 6250
Chain VS / a
Non-redundant True
Interacting RNA chains V/a
Volume 611.57 Å3
Hydrophobicity 0.113
Hydrophilicity 1.023
Buriedness 0.707
Don/acc character 1.784
SiteScore 1.009
D Score 1.030

Compound 84G
Residue . / 6252
Chain XS / a
Non-redundant True
Interacting RNA chains V/a
Volume 76.49 Å3
Hydrophobicity 0.079
Hydrophilicity 1.099
Buriedness 0.597
Don/acc character 1.467
SiteScore 0.453
D Score 0.326

Compound 84G
Residue . / 6253
Chain YS / a
Non-redundant True
Interacting RNA chains V/a
Volume 183.85 Å3
Hydrophobicity 0.085
Hydrophilicity 0.859
Buriedness 0.689
Don/acc character 3.827
SiteScore 0.615
D Score 0.543

Compound 84G
Residue . / 6254
Chain ZS / a
Non-redundant True
Interacting RNA chains V/a
Volume 292.92 Å3
Hydrophobicity 0.022
Hydrophilicity 1.073
Buriedness 0.676
Don/acc character 2.223
SiteScore 0.749
D Score 0.693

Compound 84G
Residue . / 6255
Chain AT / a
Non-redundant True
Interacting RNA chains V/a
Volume 813.94 Å3
Hydrophobicity 0.148
Hydrophilicity 1.075
Buriedness 0.689
Don/acc character 2.132
SiteScore 0.994
D Score 1.003

Compound SPM
Residue . / 6204
Chain BR / a
Non-redundant False
Interacting RNA chains V/a
Volume 297.38 Å3
Hydrophobicity 0.146
Hydrophilicity 1.240
Buriedness 0.741
Don/acc character 0.963
SiteScore 0.926
D Score 0.849