HARIBOSS

Harnessing RIBOnucleic acid - Small molecules Structures

Complex 5obm

System information

Experimental technique X-ray
Experimental resolution 3.40
System mass 6274.90 kDa
Deposition year 2017
Molecule type RNA/Protein
# RNA entities 1
Organism Saccharomyces
RCSB PDB Entry 5obm
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 LLL
Residue . / 3989
Chain VBA / 1
Non-redundant True
Interacting RNA chains B/3, A/1
Volume 519.30 Å3
Hydrophobicity 0.016
Hydrophilicity 1.422
Buriedness 0.746
Don/acc character 1.155
SiteScore 1.182
D Score 0.924

Compound LLL
Residue . / 3990
Chain WBA / 1
Non-redundant True
Interacting RNA chains C/4, A/1
Volume 522.73 Å3
Hydrophobicity 0.108
Hydrophilicity 1.502
Buriedness 0.737
Don/acc character 1.449
SiteScore 1.176
D Score 0.892

Compound LLL
Residue . / 3991
Chain XBA / 1
Non-redundant True
Interacting RNA chains C/4, A/1
Volume 458.93 Å3
Hydrophobicity 0.240
Hydrophilicity 1.549
Buriedness 0.800
Don/acc character 1.110
SiteScore 1.218
D Score 0.915

Compound LLL
Residue . / 3992
Chain YBA / 1
Non-redundant True
Interacting RNA chains A/1
Volume 443.50 Å3
Hydrophobicity 0.060
Hydrophilicity 1.895
Buriedness 0.643
Don/acc character 0.789
SiteScore 0.964
D Score 0.708

Compound LLL
Residue . / 3993
Chain ZBA / 1
Non-redundant True
Interacting RNA chains A/1
Volume 233.58 Å3
Hydrophobicity 0.025
Hydrophilicity 1.492
Buriedness 0.714
Don/acc character 1.474
SiteScore 1.028
D Score 0.712

Compound LLL
Residue . / 3994
Chain ACA / 1
Non-redundant True
Interacting RNA chains A/1
Volume 845.15 Å3
Hydrophobicity 0.216
Hydrophilicity 1.220
Buriedness 0.808
Don/acc character 1.844
SiteScore 1.073
D Score 1.027

Compound LLL
Residue . / 3995
Chain BCA / 1
Non-redundant True
Interacting RNA chains A/1
Volume 189.68 Å3
Hydrophobicity 0.058
Hydrophilicity 1.631
Buriedness 0.692
Don/acc character 0.712
SiteScore 0.876
D Score 0.478

Compound LLL
Residue . / 3996
Chain CCA / 1
Non-redundant True
Interacting RNA chains A/1
Volume 312.47 Å3
Hydrophobicity 0.040
Hydrophilicity 1.540
Buriedness 0.791
Don/acc character 0.885
SiteScore 0.858
D Score 0.651

Compound LLL
Residue . / 3997
Chain DCA / 1
Non-redundant True
Interacting RNA chains A/1
Volume -
Hydrophobicity -
Hydrophilicity -
Buriedness -
Don/acc character -
SiteScore -
D Score -

Compound LLL
Residue . / 3998
Chain ECA / 1
Non-redundant True
Interacting RNA chains C/4, A/1
Volume 529.59 Å3
Hydrophobicity 0.212
Hydrophilicity 1.305
Buriedness 0.800
Don/acc character 1.446
SiteScore 0.879
D Score 0.752

Compound LLL
Residue . / 3999
Chain FCA / 1
Non-redundant True
Interacting RNA chains A/1
Volume 251.08 Å3
Hydrophobicity 0.273
Hydrophilicity 1.157
Buriedness 0.819
Don/acc character 1.150
SiteScore 0.762
D Score 0.646

Compound LLL
Residue . / 4000
Chain GCA / 1
Non-redundant True
Interacting RNA chains A/1
Volume 231.53 Å3
Hydrophobicity 0.995
Hydrophilicity 1.567
Buriedness 0.816
Don/acc character 0.882
SiteScore 0.928
D Score 0.725

Compound LLL
Residue . / 4001
Chain HCA / 1
Non-redundant True
Interacting RNA chains A/1
Volume 435.27 Å3
Hydrophobicity 0.170
Hydrophilicity 1.073
Buriedness 0.684
Don/acc character 0.944
SiteScore 0.972
D Score 0.977

Compound LLL
Residue . / 4002
Chain ICA / 1
Non-redundant True
Interacting RNA chains A/1
Volume 418.12 Å3
Hydrophobicity 0.130
Hydrophilicity 1.248
Buriedness 0.729
Don/acc character 1.262
SiteScore 0.923
D Score 0.845

Compound LLL
Residue . / 4003
Chain JCA / 1
Non-redundant True
Interacting RNA chains A/1
Volume 248.33 Å3
Hydrophobicity 0.122
Hydrophilicity 1.200
Buriedness 0.720
Don/acc character 1.892
SiteScore 0.907
D Score 0.650

Compound LLL
Residue . / 4004
Chain KCA / 1
Non-redundant True
Interacting RNA chains B/3, A/1
Volume 684.29 Å3
Hydrophobicity 0.130
Hydrophilicity 1.323
Buriedness 0.716
Don/acc character 0.864
SiteScore 1.012
D Score 0.938

Compound LLL
Residue . / 220
Chain EDA / 3
Non-redundant True
Interacting RNA chains B/3, A/1
Volume 197.23 Å3
Hydrophobicity 0.510
Hydrophilicity 1.043
Buriedness 0.799
Don/acc character 0.760
SiteScore 0.637
D Score 0.527

Compound LLL
Residue . / 224
Chain CEA / 4
Non-redundant True
Interacting RNA chains C/4
Volume 398.22 Å3
Hydrophobicity 0.124
Hydrophilicity 1.213
Buriedness 0.775
Don/acc character 1.523
SiteScore 0.816
D Score 0.707

Compound LLL
Residue . / 404
Chain LEA / L3
Non-redundant True
Interacting RNA chains A/1
Volume 178.02 Å3
Hydrophobicity 0.038
Hydrophilicity 1.270
Buriedness 0.767
Don/acc character 3.776
SiteScore 0.672
D Score 0.507

Compound LLL
Residue . / 2043
Chain OMA / 2
Non-redundant True
Interacting RNA chains SA/2
Volume 559.43 Å3
Hydrophobicity 0.292
Hydrophilicity 1.404
Buriedness 0.844
Don/acc character 1.251
SiteScore 1.198
D Score 0.925

Compound LLL
Residue . / 2044
Chain PMA / 2
Non-redundant True
Interacting RNA chains SA/2
Volume 128.28 Å3
Hydrophobicity 0.076
Hydrophilicity 1.206
Buriedness 0.710
Don/acc character 1.273
SiteScore 0.679
D Score 0.359

Compound LLL
Residue . / 2045
Chain QMA / 2
Non-redundant True
Interacting RNA chains SA/2
Volume 173.22 Å3
Hydrophobicity 0.206
Hydrophilicity 1.684
Buriedness 0.861
Don/acc character 1.092
SiteScore 0.972
D Score 0.539

Compound LLL
Residue . / 4151
Chain DQB / 5
Non-redundant True
Interacting RNA chains CC/7, BC/5
Volume 552.23 Å3
Hydrophobicity 0.089
Hydrophilicity 1.217
Buriedness 0.750
Don/acc character 1.291
SiteScore 1.184
D Score 0.993

Compound LLL
Residue . / 4152
Chain EQB / 5
Non-redundant True
Interacting RNA chains CC/7, BC/5
Volume 751.51 Å3
Hydrophobicity 0.108
Hydrophilicity 1.371
Buriedness 0.691
Don/acc character 0.827
SiteScore 0.995
D Score 0.908

Compound LLL
Residue . / 4153
Chain FQB / 5
Non-redundant True
Interacting RNA chains DC/8, BC/5
Volume 773.81 Å3
Hydrophobicity 0.127
Hydrophilicity 1.438
Buriedness 0.709
Don/acc character 0.896
SiteScore 1.158
D Score 0.897

Compound LLL
Residue . / 4154
Chain GQB / 5
Non-redundant True
Interacting RNA chains DC/8, BC/5
Volume 709.32 Å3
Hydrophobicity 0.149
Hydrophilicity 1.533
Buriedness 0.755
Don/acc character 1.099
SiteScore 1.188
D Score 0.893

Compound LLL
Residue . / 4155
Chain HQB / 5
Non-redundant True
Interacting RNA chains BC/5
Volume 314.53 Å3
Hydrophobicity 0.130
Hydrophilicity 0.935
Buriedness 0.607
Don/acc character 2.101
SiteScore 0.886
D Score 0.905

Compound LLL
Residue . / 4156
Chain IQB / 5
Non-redundant True
Interacting RNA chains BC/5
Volume 146.12 Å3
Hydrophobicity 0.014
Hydrophilicity 0.978
Buriedness 0.623
Don/acc character 3.663
SiteScore 0.787
D Score 0.578

Compound LLL
Residue . / 4157
Chain JQB / 5
Non-redundant True
Interacting RNA chains BC/5
Volume 301.84 Å3
Hydrophobicity 0.000
Hydrophilicity 1.088
Buriedness 0.710
Don/acc character 3.283
SiteScore 0.978
D Score 0.781

Compound LLL
Residue . / 4158
Chain KQB / 5
Non-redundant True
Interacting RNA chains BC/5
Volume 550.17 Å3
Hydrophobicity 0.009
Hydrophilicity 2.138
Buriedness 0.799
Don/acc character 0.571
SiteScore 1.111
D Score 0.586

Compound LLL
Residue . / 4159
Chain LQB / 5
Non-redundant True
Interacting RNA chains BC/5
Volume 585.84 Å3
Hydrophobicity 0.164
Hydrophilicity 1.344
Buriedness 0.825
Don/acc character 1.352
SiteScore 0.895
D Score 0.754

Compound LLL
Residue . / 4160
Chain MQB / 5
Non-redundant True
Interacting RNA chains BC/5
Volume 214.03 Å3
Hydrophobicity 0.078
Hydrophilicity 1.646
Buriedness 0.826
Don/acc character 0.535
SiteScore 0.760
D Score 0.482

Compound LLL
Residue . / 4161
Chain NQB / 5
Non-redundant True
Interacting RNA chains BC/5
Volume 40.82 Å3
Hydrophobicity 0.166
Hydrophilicity 0.669
Buriedness 0.532
Don/acc character 2.956
SiteScore 0.662
D Score 0.466

Compound LLL
Residue . / 4162
Chain OQB / 5
Non-redundant True
Interacting RNA chains BC/5
Volume 245.25 Å3
Hydrophobicity 0.067
Hydrophilicity 1.153
Buriedness 0.676
Don/acc character 1.404
SiteScore 0.811
D Score 0.746

Compound LLL
Residue . / 4163
Chain PQB / 5
Non-redundant True
Interacting RNA chains BC/5
Volume 182.13 Å3
Hydrophobicity 0.006
Hydrophilicity 1.465
Buriedness 0.657
Don/acc character 1.328
SiteScore 0.859
D Score 0.518

Compound LLL
Residue . / 4164
Chain QQB / 5
Non-redundant True
Interacting RNA chains BC/5
Volume 399.60 Å3
Hydrophobicity 0.460
Hydrophilicity 1.054
Buriedness 0.837
Don/acc character 1.771
SiteScore 0.942
D Score 0.904

Compound LLL
Residue . / 4165
Chain RQB / 5
Non-redundant True
Interacting RNA chains BC/5
Volume 268.57 Å3
Hydrophobicity 0.092
Hydrophilicity 1.617
Buriedness 0.803
Don/acc character 0.712
SiteScore 0.795
D Score 0.542

Compound LLL
Residue . / 4166
Chain SQB / 5
Non-redundant True
Interacting RNA chains BC/5
Volume 233.58 Å3
Hydrophobicity 0.207
Hydrophilicity 1.008
Buriedness 0.708
Don/acc character 3.766
SiteScore 0.870
D Score 0.660

Compound LLL
Residue . / 4167
Chain TQB / 5
Non-redundant True
Interacting RNA chains BC/5
Volume 566.29 Å3
Hydrophobicity 0.069
Hydrophilicity 1.289
Buriedness 0.711
Don/acc character 1.282
SiteScore 1.155
D Score 0.941

Compound LLL
Residue . / 4168
Chain UQB / 5
Non-redundant True
Interacting RNA chains BC/5
Volume 503.52 Å3
Hydrophobicity 0.359
Hydrophilicity 1.023
Buriedness 0.795
Don/acc character 1.572
SiteScore 0.827
D Score 0.774

Compound LLL
Residue . / 4169
Chain VQB / 5
Non-redundant True
Interacting RNA chains BC/5
Volume 743.62 Å3
Hydrophobicity 0.124
Hydrophilicity 1.262
Buriedness 0.776
Don/acc character 2.118
SiteScore 1.202
D Score 0.994

Compound LLL
Residue . / 4170
Chain WQB / 5
Non-redundant True
Interacting RNA chains BC/5
Volume 624.60 Å3
Hydrophobicity 0.158
Hydrophilicity 0.928
Buriedness 0.667
Don/acc character 2.677
SiteScore 1.151
D Score 1.037

Compound LLL
Residue . / 4171
Chain XQB / 5
Non-redundant True
Interacting RNA chains BC/5
Volume 215.06 Å3
Hydrophobicity 0.029
Hydrophilicity 2.256
Buriedness 0.758
Don/acc character 0.553
SiteScore 0.681
D Score 0.199

Compound LLL
Residue . / 4172
Chain YQB / 5
Non-redundant True
Interacting RNA chains BC/5
Volume 198.94 Å3
Hydrophobicity 0.027
Hydrophilicity 1.148
Buriedness 0.687
Don/acc character 2.609
SiteScore 0.867
D Score 0.625

Compound LLL
Residue . / 4173
Chain ZQB / 5
Non-redundant True
Interacting RNA chains BC/5
Volume 94.67 Å3
Hydrophobicity 0.023
Hydrophilicity 1.421
Buriedness 0.670
Don/acc character 0.407
SiteScore 0.850
D Score 0.518

Compound LLL
Residue . / 4174
Chain ARB / 5
Non-redundant True
Interacting RNA chains BC/5
Volume 304.58 Å3
Hydrophobicity 0.076
Hydrophilicity 1.840
Buriedness 0.768
Don/acc character 0.660
SiteScore 0.772
D Score 0.349

Compound LLL
Residue . / 4175
Chain BRB / 5
Non-redundant True
Interacting RNA chains BC/5
Volume 664.39 Å3
Hydrophobicity 0.117
Hydrophilicity 1.605
Buriedness 0.765
Don/acc character 1.228
SiteScore 1.092
D Score 0.745

Compound LLL
Residue . / 4176
Chain CRB / 5
Non-redundant True
Interacting RNA chains BC/5
Volume 202.71 Å3
Hydrophobicity 0.211
Hydrophilicity 1.401
Buriedness 0.835
Don/acc character 2.434
SiteScore 0.670
D Score 0.443

Compound LLL
Residue . / 4177
Chain DRB / 5
Non-redundant True
Interacting RNA chains BC/5
Volume 344.72 Å3
Hydrophobicity 0.069
Hydrophilicity 1.254
Buriedness 0.753
Don/acc character 3.554
SiteScore 1.009
D Score 0.695

Compound LLL
Residue . / 4178
Chain ERB / 5
Non-redundant True
Interacting RNA chains BC/5
Volume 139.60 Å3
Hydrophobicity 0.262
Hydrophilicity 1.230
Buriedness 0.724
Don/acc character 0.708
SiteScore 0.778
D Score 0.474

Compound LLL
Residue . / 231
Chain JSB / 7
Non-redundant True
Interacting RNA chains CC/7
Volume 67.91 Å3
Hydrophobicity 0.028
Hydrophilicity 1.183
Buriedness 0.620
Don/acc character 1.483
SiteScore 0.517
D Score 0.374

Compound LLL
Residue . / 232
Chain KSB / 7
Non-redundant True
Interacting RNA chains CC/7, BC/5
Volume 345.06 Å3
Hydrophobicity 0.322
Hydrophilicity 0.905
Buriedness 0.690
Don/acc character 2.096
SiteScore 1.171
D Score 1.059

Compound LLL
Residue . / 233
Chain LSB / 7
Non-redundant True
Interacting RNA chains CC/7
Volume 325.16 Å3
Hydrophobicity 0.074
Hydrophilicity 1.106
Buriedness 0.715
Don/acc character 0.817
SiteScore 0.797
D Score 0.733

Compound LLL
Residue . / 221
Chain GTB / 8
Non-redundant True
Interacting RNA chains DC/8
Volume 320.36 Å3
Hydrophobicity 0.158
Hydrophilicity 1.201
Buriedness 0.786
Don/acc character 1.534
SiteScore 0.801
D Score 0.689

Compound LLL
Residue . / 222
Chain HTB / 8
Non-redundant True
Interacting RNA chains DC/8, BC/5
Volume 460.65 Å3
Hydrophobicity 0.085
Hydrophilicity 1.428
Buriedness 0.798
Don/acc character 1.237
SiteScore 0.797
D Score 0.608

Compound LLL
Residue . / 412
Chain YTB / l3
Non-redundant True
Interacting RNA chains BC/5
Volume 553.60 Å3
Hydrophobicity 0.158
Hydrophilicity 1.157
Buriedness 0.708
Don/acc character 2.086
SiteScore 1.157
D Score 0.988

Compound LLL
Residue . / 2164
Chain AIC / 6
Non-redundant True
Interacting RNA chains WD/6
Volume 430.12 Å3
Hydrophobicity 0.158
Hydrophilicity 1.160
Buriedness 0.688
Don/acc character 1.148
SiteScore 1.143
D Score 0.975

Compound LLL
Residue . / 2165
Chain BIC / 6
Non-redundant True
Interacting RNA chains WD/6
Volume 454.48 Å3
Hydrophobicity 0.148
Hydrophilicity 1.022
Buriedness 0.726
Don/acc character 2.840
SiteScore 1.040
D Score 0.872

Compound LLL
Residue . / 2166
Chain CIC / 6
Non-redundant True
Interacting RNA chains WD/6
Volume 237.70 Å3
Hydrophobicity 0.084
Hydrophilicity 1.163
Buriedness 0.793
Don/acc character 3.211
SiteScore 0.702
D Score 0.537

Compound LLL
Residue . / 2167
Chain DIC / 6
Non-redundant True
Interacting RNA chains WD/6
Volume 237.36 Å3
Hydrophobicity 0.014
Hydrophilicity 1.143
Buriedness 0.746
Don/acc character 2.884
SiteScore 0.643
D Score 0.323

Compound LLL
Residue . / 2168
Chain EIC / 6
Non-redundant True
Interacting RNA chains WD/6, BC/5
Volume 514.84 Å3
Hydrophobicity 0.143
Hydrophilicity 1.872
Buriedness 0.677
Don/acc character 0.583
SiteScore 0.986
D Score 0.736

Compound LLL
Residue . / 2169
Chain FIC / 6
Non-redundant True
Interacting RNA chains WD/6
Volume 687.03 Å3
Hydrophobicity 0.160
Hydrophilicity 1.375
Buriedness 0.794
Don/acc character 1.154
SiteScore 1.214
D Score 0.968

Compound LLL
Residue . / 2170
Chain GIC / 6
Non-redundant True
Interacting RNA chains WD/6
Volume 276.12 Å3
Hydrophobicity 0.112
Hydrophilicity 0.977
Buriedness 0.668
Don/acc character 1.886
SiteScore 0.958
D Score 0.786

Compound LLL
Residue . / 2171
Chain HIC / 6
Non-redundant True
Interacting RNA chains WD/6
Volume 149.89 Å3
Hydrophobicity 0.181
Hydrophilicity 1.145
Buriedness 0.685
Don/acc character 1.554
SiteScore 0.782
D Score 0.517

Compound LLL
Residue . / 2172
Chain IIC / 6
Non-redundant True
Interacting RNA chains WD/6
Volume 530.62 Å3
Hydrophobicity 0.413
Hydrophilicity 0.940
Buriedness 0.710
Don/acc character 1.867
SiteScore 1.170
D Score 1.050

Compound LLL
Residue . / 2173
Chain JIC / 6
Non-redundant True
Interacting RNA chains WD/6
Volume 380.39 Å3
Hydrophobicity 0.062
Hydrophilicity 1.273
Buriedness 0.778
Don/acc character 1.445
SiteScore 0.546
D Score 0.483

Compound LLL
Residue . / 2174
Chain KIC / 6
Non-redundant True
Interacting RNA chains WD/6, BC/5
Volume 266.17 Å3
Hydrophobicity 0.226
Hydrophilicity 1.050
Buriedness 0.749
Don/acc character 1.443
SiteScore 0.735
D Score 0.663

Compound LLL
Residue . / 2175
Chain LIC / 6
Non-redundant True
Interacting RNA chains WD/6
Volume 599.56 Å3
Hydrophobicity 0.193
Hydrophilicity 1.236
Buriedness 0.723
Don/acc character 1.986
SiteScore 1.166
D Score 0.971

Compound LLL
Residue . / 2176
Chain MIC / 6
Non-redundant True
Interacting RNA chains WD/6
Volume 444.87 Å3
Hydrophobicity 0.191
Hydrophilicity 1.206
Buriedness 0.747
Don/acc character 2.648
SiteScore 1.183
D Score 0.995