HARIBOSS

Harnessing RIBOnucleic acid - Small molecules Structures

Complex 5ndv

System information

Experimental technique X-ray
Experimental resolution 3.30
System mass 6227.43 kDa
Deposition year 2017
Molecule type RNA/Protein
# RNA entities 3
Organism Saccharomyces
RCSB PDB Entry 5ndv
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 PAR
Residue . / 3401
Chain AF / 1
Non-redundant True
Interacting RNA chains A/1
Volume 214.03 Å3
Hydrophobicity 0.078
Hydrophilicity 1.271
Buriedness 0.723
Don/acc character 3.253
SiteScore 0.847
D Score 0.741

Compound PAR
Residue . / 3406
Chain FF / 1
Non-redundant True
Interacting RNA chains A/1
Volume 256.91 Å3
Hydrophobicity 0.031
Hydrophilicity 1.170
Buriedness 0.655
Don/acc character 1.973
SiteScore 0.847
D Score 0.792

Compound PAR
Residue . / 3423
Chain WF / 1
Non-redundant True
Interacting RNA chains A/1
Volume 915.47 Å3
Hydrophobicity 0.075
Hydrophilicity 1.177
Buriedness 0.709
Don/acc character 1.504
SiteScore 1.007
D Score 0.982

Compound PAR
Residue . / 3432
Chain FG / 1
Non-redundant True
Interacting RNA chains A/1
Volume 300.81 Å3
Hydrophobicity 0.144
Hydrophilicity 1.075
Buriedness 0.640
Don/acc character 5.919
SiteScore 0.892
D Score 0.885

Compound PAR
Residue . / 3434
Chain HG / 1
Non-redundant True
Interacting RNA chains A/1
Volume 446.59 Å3
Hydrophobicity 0.081
Hydrophilicity 1.122
Buriedness 0.661
Don/acc character 1.839
SiteScore 0.975
D Score 0.970

Compound PAR
Residue . / 202
Chain MKA / 4
Non-redundant True
Interacting RNA chains C/4
Volume 216.78 Å3
Hydrophobicity 0.018
Hydrophilicity 1.249
Buriedness 0.666
Don/acc character 1.770
SiteScore 0.789
D Score 0.690

Compound PAR
Residue . / 1901
Chain VPA / 2
Non-redundant True
Interacting RNA chains SA/2
Volume 346.43 Å3
Hydrophobicity 0.114
Hydrophilicity 1.453
Buriedness 0.711
Don/acc character 2.295
SiteScore 1.009
D Score 0.893

Compound PAR
Residue . / 3402
Chain TYA / 5
Non-redundant True
Interacting RNA chains AC/5
Volume 393.08 Å3
Hydrophobicity 0.065
Hydrophilicity 1.108
Buriedness 0.663
Don/acc character 1.813
SiteScore 0.977
D Score 0.977

Compound PAR
Residue . / 3405
Chain WYA / 5
Non-redundant True
Interacting RNA chains AC/5
Volume 250.05 Å3
Hydrophobicity 0.043
Hydrophilicity 1.329
Buriedness 0.718
Don/acc character 3.558
SiteScore 0.848
D Score 0.725

Compound PAR
Residue . / 3419
Chain KZA / 5
Non-redundant True
Interacting RNA chains AC/5
Volume 429.78 Å3
Hydrophobicity 0.084
Hydrophilicity 1.182
Buriedness 0.707
Don/acc character 1.990
SiteScore 0.964
D Score 0.925

Compound PAR
Residue . / 3426
Chain RZA / 5
Non-redundant True
Interacting RNA chains AC/5
Volume 241.13 Å3
Hydrophobicity 0.034
Hydrophilicity 1.256
Buriedness 0.668
Don/acc character 3.788
SiteScore 0.860
D Score 0.778

Compound PAR
Residue . / 3428
Chain TZA / 5
Non-redundant True
Interacting RNA chains AC/5
Volume -
Hydrophobicity -
Hydrophilicity -
Buriedness -
Don/acc character -
SiteScore -
D Score -

Compound PAR
Residue . / 1903
Chain TFC / 6
Non-redundant True
Interacting RNA chains SD/6
Volume 1191.92 Å3
Hydrophobicity 0.107
Hydrophilicity 1.247
Buriedness 0.724
Don/acc character 2.239
SiteScore 1.017
D Score 0.968