HARIBOSS

Harnessing RIBOnucleic acid - Small molecules Structures

Complex 8ifb

System information

Experimental technique Electron Microscopy
Experimental resolution 2.43
System mass 2211.26 kDa
Deposition year 2023
Molecule type RNA/Protein
# RNA entities 6
Organism Escherichia
RCSB PDB Entry 8ifb
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 84D
Residue . / 1738
Chain KG / A
Non-redundant True
Interacting RNA chains A/A
Volume 232.90 Å3
Hydrophobicity 0.094
Hydrophilicity 0.997
Buriedness 0.684
Don/acc character 3.764
SiteScore 0.843
D Score 0.826

Compound 84D
Residue . / 1739
Chain LG / A
Non-redundant True
Interacting RNA chains A/A
Volume -
Hydrophobicity -
Hydrophilicity -
Buriedness -
Don/acc character -
SiteScore -
D Score -

Compound 84D
Residue . / 3255
Chain RQ / a
Non-redundant True
Interacting RNA chains A/A, V/a
Volume 217.46 Å3
Hydrophobicity 0.335
Hydrophilicity 1.050
Buriedness 0.702
Don/acc character 2.654
SiteScore 0.933
D Score 0.930

Compound 84D
Residue . / 3256
Chain SQ / a
Non-redundant True
Interacting RNA chains V/a
Volume 89.18 Å3
Hydrophobicity 0.000
Hydrophilicity 0.824
Buriedness 0.650
Don/acc character 4.717
SiteScore 0.440
D Score 0.331

Compound 84D
Residue . / 3257
Chain TQ / a
Non-redundant True
Interacting RNA chains V/a
Volume 277.14 Å3
Hydrophobicity 0.000
Hydrophilicity 1.269
Buriedness 0.687
Don/acc character 1.557
SiteScore 0.735
D Score 0.608

Compound 84D
Residue . / 3258
Chain UQ / a
Non-redundant True
Interacting RNA chains V/a
Volume 534.39 Å3
Hydrophobicity 0.076
Hydrophilicity 1.026
Buriedness 0.698
Don/acc character 3.597
SiteScore 0.909
D Score 0.904

Compound 84D
Residue . / 3260
Chain WQ / a
Non-redundant True
Interacting RNA chains V/a
Volume 644.84 Å3
Hydrophobicity 0.049
Hydrophilicity 1.382
Buriedness 0.729
Don/acc character 1.277
SiteScore 1.021
D Score 0.927

Compound 84D
Residue . / 3261
Chain XQ / a
Non-redundant True
Interacting RNA chains V/a
Volume 380.73 Å3
Hydrophobicity 0.092
Hydrophilicity 1.039
Buriedness 0.667
Don/acc character 1.805
SiteScore 0.800
D Score 0.771

Compound 84D
Residue . / 3262
Chain YQ / a
Non-redundant True
Interacting RNA chains V/a
Volume 668.16 Å3
Hydrophobicity 0.047
Hydrophilicity 1.086
Buriedness 0.665
Don/acc character 1.734
SiteScore 0.978
D Score 0.985

Compound SPM
Residue . / 3180
Chain UN / a
Non-redundant False
Interacting RNA chains V/a
Volume 321.05 Å3
Hydrophobicity 0.210
Hydrophilicity 1.237
Buriedness 0.755
Don/acc character 1.180
SiteScore 0.878
D Score 0.784