HARIBOSS

Harnessing RIBOnucleic acid - Small molecules Structures

Complex 5ndw

System information

Experimental technique X-ray
Experimental resolution 3.70
System mass 6188.11 kDa
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

Compound 8UZ
Residue . / 3887
Chain UX / 1
Non-redundant True
Interacting RNA chains A/1
Volume 160.52 Å3
Hydrophobicity 0.081
Hydrophilicity 0.989
Buriedness 0.663
Don/acc character 1.906
SiteScore 0.547
D Score 0.452

Compound 8UZ
Residue . / 3888
Chain VX / 1
Non-redundant True
Interacting RNA chains A/1
Volume 43.22 Å3
Hydrophobicity 0.077
Hydrophilicity 0.950
Buriedness 0.620
Don/acc character 1.397
SiteScore 0.440
D Score 0.328

Compound 8UZ
Residue . / 3889
Chain WX / 1
Non-redundant True
Interacting RNA chains A/1
Volume 125.54 Å3
Hydrophobicity 0.893
Hydrophilicity 1.036
Buriedness 0.745
Don/acc character 0.754
SiteScore 0.791
D Score 0.740

Compound 8UZ
Residue . / 3893
Chain AY / 1
Non-redundant True
Interacting RNA chains A/1
Volume 417.43 Å3
Hydrophobicity 0.032
Hydrophilicity 1.254
Buriedness 0.718
Don/acc character 5.745
SiteScore 0.928
D Score 0.852

Compound 8UZ
Residue . / 3894
Chain BY / 1
Non-redundant True
Interacting RNA chains A/1
Volume 691.83 Å3
Hydrophobicity 0.125
Hydrophilicity 1.197
Buriedness 0.715
Don/acc character 1.690
SiteScore 1.011
D Score 0.979

Compound 8UZ
Residue . / 2029
Chain BDA / 2
Non-redundant True
Interacting RNA chains B/2
Volume 525.82 Å3
Hydrophobicity 0.150
Hydrophilicity 1.104
Buriedness 0.700
Don/acc character 1.764
SiteScore 1.001
D Score 1.000

Compound 8UZ
Residue . / 2031
Chain DDA / 2
Non-redundant True
Interacting RNA chains B/2
Volume 199.97 Å3
Hydrophobicity 0.055
Hydrophilicity 1.343
Buriedness 0.750
Don/acc character 0.920
SiteScore 0.621
D Score 0.422

Compound 8UZ
Residue . / 220
Chain LEA / 4
Non-redundant True
Interacting RNA chains D/4, A/1
Volume 705.89 Å3
Hydrophobicity 0.078
Hydrophilicity 1.190
Buriedness 0.692
Don/acc character 1.039
SiteScore 0.996
D Score 0.968

Compound 8UZ
Residue . / 3851
Chain UVA / 5
Non-redundant True
Interacting RNA chains E/5
Volume 262.39 Å3
Hydrophobicity 0.013
Hydrophilicity 1.139
Buriedness 0.669
Don/acc character 1.387
SiteScore 0.825
D Score 0.770

Compound 8UZ
Residue . / 3855
Chain YVA / 5
Non-redundant True
Interacting RNA chains E/5
Volume 313.84 Å3
Hydrophobicity 0.109
Hydrophilicity 1.132
Buriedness 0.680
Don/acc character 1.646
SiteScore 0.823
D Score 0.767

Compound 8UZ
Residue . / 3857
Chain AWA / 5
Non-redundant True
Interacting RNA chains E/5
Volume 49.73 Å3
Hydrophobicity 0.199
Hydrophilicity 1.109
Buriedness 0.579
Don/acc character 2.784
SiteScore 0.471
D Score 0.350