HARIBOSS

Harnessing RIBOnucleic acid – Small molecules Structures


Complex 5ndw

System information

Experimental technique X-ray
Experimental resolution 3.70
System mass 6188.11
Deposition year 2017
Molecule type RNA/protein
# RNA entities 3
Organism Saccharomyces
RCSB PDB Entry 5ndw
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

Pocket 8UZ_.:UX/3887:1

Compound 8UZ
Non-redundant True
Interacting RNA chains A/1
Volume 118.33
Hydrophobicity 0.053
Hydrophilicity 1.182
Buriedness 0.674
Don/acc character 2.939
SiteScore 0.505
D Score 0.344

Pocket 8UZ_.:VX/3888:1

Compound 8UZ
Non-redundant True
Interacting RNA chains A/1
Volume 39.44
Hydrophobicity 0.000
Hydrophilicity 1.061
Buriedness 0.624
Don/acc character 0.721
SiteScore 0.425
D Score 0.294

Pocket 8UZ_.:WX/3889:1

Compound 8UZ
Non-redundant True
Interacting RNA chains A/1
Volume 124.85
Hydrophobicity 0.672
Hydrophilicity 1.108
Buriedness 0.743
Don/acc character 0.298
SiteScore 0.778
D Score 0.701

Pocket 8UZ_.:AY/3893:1

Compound 8UZ
Non-redundant True
Interacting RNA chains A/1
Volume 382.44
Hydrophobicity 0.014
Hydrophilicity 1.304
Buriedness 0.717
Don/acc character 0.701
SiteScore 0.931
D Score 0.840

Pocket 8UZ_.:BY/3894:1

Compound 8UZ
Non-redundant True
Interacting RNA chains A/1
Volume 448.64
Hydrophobicity 0.250
Hydrophilicity 1.102
Buriedness 0.721
Don/acc character 0.992
SiteScore 1.012
D Score 1.009

Pocket 8UZ_.:BDA/2029:2

Compound 8UZ
Non-redundant True
Interacting RNA chains B/2
Volume 508.33
Hydrophobicity 0.105
Hydrophilicity 1.264
Buriedness 0.709
Don/acc character 0.656
SiteScore 1.007
D Score 0.953

Pocket 8UZ_.:DDA/2031:2

Compound 8UZ
Non-redundant True
Interacting RNA chains B/2
Volume 198.94
Hydrophobicity 0.523
Hydrophilicity 1.107
Buriedness 0.752
Don/acc character 0.514
SiteScore 0.662
D Score 0.551

Pocket 8UZ_.:LEA/220:4

Compound 8UZ
Non-redundant True
Interacting RNA chains D/4, A/1
Volume 682.91
Hydrophobicity 0.118
Hydrophilicity 1.340
Buriedness 0.700
Don/acc character 0.775
SiteScore 1.001
D Score 0.923

Pocket 8UZ_.:UVA/3851:5

Compound 8UZ
Non-redundant True
Interacting RNA chains E/5
Volume 257.94
Hydrophobicity 0.171
Hydrophilicity 1.070
Buriedness 0.685
Don/acc character 1.011
SiteScore 0.787
D Score 0.740

Pocket 8UZ_.:YVA/3855:5

Compound 8UZ
Non-redundant True
Interacting RNA chains E/5
Volume 308.01
Hydrophobicity 0.245
Hydrophilicity 1.153
Buriedness 0.693
Don/acc character 1.832
SiteScore 0.807
D Score 0.737

Pocket 8UZ_.:AWA/3857:5

Compound 8UZ
Non-redundant True
Interacting RNA chains E/5
Volume 48.02
Hydrophobicity 0.282
Hydrophilicity 0.975
Buriedness 0.578
Don/acc character 1.826
SiteScore 0.502
D Score 0.417