HARIBOSS

Harnessing RIBOnucleic acid - Small molecules Structures

Complex 9e71

System information

Experimental technique Electron Microscopy
Experimental resolution 2.36
System mass 2559.27 kDa
Deposition year 2024
Molecule type RNA/Protein
# RNA entities 1
Organism Pyrobaculum
RCSB PDB Entry 9e71
Reference Nissley Amos J., Shulgina Yekaterina, Kivimae Roan W., Downing Blake E., Penev Petar I., Banfield Jillian F., Nayak Dipti D., Cate Jamie H. D.. . Structure of an archaeal ribosome reveals a divergent active site and hibernation factor Nature Microbiology

Compound SPM
Residue . / 3101
Chain RB / 1
Non-redundant True
Interacting RNA chains B/1
Volume 329.28 Å3
Hydrophobicity 0.137
Hydrophilicity 1.487
Buriedness 0.646
Don/acc character 1.039
SiteScore 1.115
D Score 0.843

Compound SPM
Residue . / 3102
Chain SB / 1
Non-redundant True
Interacting RNA chains B/1
Volume 294.98 Å3
Hydrophobicity 0.228
Hydrophilicity 1.095
Buriedness 0.688
Don/acc character 2.122
SiteScore 0.993
D Score 0.996

Compound SPM
Residue . / 3103
Chain TB / 1
Non-redundant True
Interacting RNA chains B/1
Volume 1095.54 Å3
Hydrophobicity 0.080
Hydrophilicity 2.032
Buriedness 0.853
Don/acc character 0.819
SiteScore 1.103
D Score 0.789

Compound SPM
Residue . / 3104
Chain UB / 1
Non-redundant True
Interacting RNA chains B/1
Volume 710.35 Å3
Hydrophobicity 0.253
Hydrophilicity 1.416
Buriedness 0.880
Don/acc character 1.128
SiteScore 1.122
D Score 1.006

Compound SPM
Residue . / 3105
Chain VB / 1
Non-redundant True
Interacting RNA chains B/1
Volume 447.62 Å3
Hydrophobicity 0.080
Hydrophilicity 1.180
Buriedness 0.767
Don/acc character 1.540
SiteScore 1.196
D Score 1.016

Compound SPM
Residue . / 3106
Chain WB / 1
Non-redundant True
Interacting RNA chains B/1
Volume 494.61 Å3
Hydrophobicity 0.296
Hydrophilicity 1.214
Buriedness 0.677
Don/acc character 1.450
SiteScore 1.136
D Score 0.951

Compound SPM
Residue . / 3107
Chain XB / 1
Non-redundant True
Interacting RNA chains B/1
Volume 495.64 Å3
Hydrophobicity 0.053
Hydrophilicity 1.950
Buriedness 0.815
Don/acc character 0.808
SiteScore 1.037
D Score 0.740

Compound SPM
Residue . / 3108
Chain YB / 1
Non-redundant True
Interacting RNA chains B/1
Volume 791.30 Å3
Hydrophobicity 0.173
Hydrophilicity 1.361
Buriedness 0.799
Don/acc character 1.710
SiteScore 1.067
D Score 0.976

Compound SPM
Residue . / 3109
Chain ZB / 1
Non-redundant True
Interacting RNA chains B/1
Volume 385.19 Å3
Hydrophobicity 0.035
Hydrophilicity 2.275
Buriedness 0.864
Don/acc character 0.950
SiteScore 0.912
D Score 0.461

Compound SPM
Residue . / 3110
Chain AC / 1
Non-redundant True
Interacting RNA chains B/1
Volume 939.82 Å3
Hydrophobicity 0.157
Hydrophilicity 1.640
Buriedness 0.850
Don/acc character 1.029
SiteScore 1.251
D Score 0.915

Compound SPM
Residue . / 3111
Chain BC / 1
Non-redundant True
Interacting RNA chains B/1
Volume 653.42 Å3
Hydrophobicity 0.102
Hydrophilicity 1.486
Buriedness 0.832
Don/acc character 1.547
SiteScore 1.240
D Score 0.955

Compound SPM
Residue . / 3112
Chain CC / 1
Non-redundant True
Interacting RNA chains B/1
Volume 369.41 Å3
Hydrophobicity 0.019
Hydrophilicity 1.386
Buriedness 0.624
Don/acc character 2.357
SiteScore 1.100
D Score 0.863

Compound SPM
Residue . / 3113
Chain DC / 1
Non-redundant True
Interacting RNA chains B/1
Volume 456.53 Å3
Hydrophobicity 0.045
Hydrophilicity 1.371
Buriedness 0.811
Don/acc character 2.071
SiteScore 0.840
D Score 0.677

Compound SPM
Residue . / 3114
Chain EC / 1
Non-redundant True
Interacting RNA chains B/1
Volume 276.12 Å3
Hydrophobicity 0.257
Hydrophilicity 0.880
Buriedness 0.648
Don/acc character 3.051
SiteScore 0.994
D Score 1.037

Compound SPM
Residue . / 3115
Chain FC / 1
Non-redundant True
Interacting RNA chains B/1
Volume 186.94 Å3
Hydrophobicity 0.139
Hydrophilicity 1.604
Buriedness 0.809
Don/acc character 0.677
SiteScore 0.625
D Score 0.327

Compound SPM
Residue . / 3116
Chain GC / 1
Non-redundant True
Interacting RNA chains B/1
Volume 788.21 Å3
Hydrophobicity 0.579
Hydrophilicity 1.156
Buriedness 0.857
Don/acc character 2.169
SiteScore 1.256
D Score 1.077

Compound SPM
Residue . / 3117
Chain HC / 1
Non-redundant True
Interacting RNA chains B/1
Volume 304.58 Å3
Hydrophobicity 0.157
Hydrophilicity 0.865
Buriedness 0.659
Don/acc character 2.189
SiteScore 1.051
D Score 0.916

Compound SPM
Residue . / 3118
Chain IC / 1
Non-redundant True
Interacting RNA chains B/1
Volume 633.52 Å3
Hydrophobicity 0.191
Hydrophilicity 1.088
Buriedness 0.769
Don/acc character 4.421
SiteScore 1.197
D Score 1.046

Compound SPM
Residue . / 3119
Chain JC / 1
Non-redundant True
Interacting RNA chains B/1
Volume 178.70 Å3
Hydrophobicity 0.000
Hydrophilicity 1.315
Buriedness 0.662
Don/acc character 1.984
SiteScore 0.941
D Score 0.672

Compound SPM
Residue . / 3120
Chain KC / 1
Non-redundant True
Interacting RNA chains B/1
Volume 205.80 Å3
Hydrophobicity 0.088
Hydrophilicity 0.948
Buriedness 0.675
Don/acc character 3.018
SiteScore 0.727
D Score 0.683

Compound SPM
Residue . / 3121
Chain LC / 1
Non-redundant True
Interacting RNA chains B/1
Volume 557.38 Å3
Hydrophobicity 0.584
Hydrophilicity 1.152
Buriedness 0.868
Don/acc character 1.242
SiteScore 1.264
D Score 1.085

Compound SPM
Residue . / 3122
Chain MC / 1
Non-redundant True
Interacting RNA chains B/1
Volume 663.71 Å3
Hydrophobicity 0.031
Hydrophilicity 1.645
Buriedness 0.788
Don/acc character 1.258
SiteScore 1.210
D Score 0.877

Compound SPM
Residue . / 3123
Chain NC / 1
Non-redundant True
Interacting RNA chains B/1
Volume 458.25 Å3
Hydrophobicity 0.085
Hydrophilicity 1.288
Buriedness 0.771
Don/acc character 1.027
SiteScore 1.109
D Score 0.867

Compound SPM
Residue . / 3124
Chain OC / 1
Non-redundant True
Interacting RNA chains B/1
Volume 36.02 Å3
Hydrophobicity 0.065
Hydrophilicity 1.022
Buriedness 0.539
Don/acc character 4.156
SiteScore 0.478
D Score 0.200

Compound SPM
Residue . / 3125
Chain PC / 1
Non-redundant True
Interacting RNA chains B/1
Volume 513.81 Å3
Hydrophobicity 0.101
Hydrophilicity 1.509
Buriedness 0.806
Don/acc character 1.255
SiteScore 1.169
D Score 0.863

Compound SPM
Residue . / 3126
Chain QC / 1
Non-redundant True
Interacting RNA chains B/1
Volume 688.74 Å3
Hydrophobicity 0.087
Hydrophilicity 1.945
Buriedness 0.816
Don/acc character 1.128
SiteScore 1.229
D Score 0.796

Compound SPM
Residue . / 3127
Chain RC / 1
Non-redundant True
Interacting RNA chains B/1
Volume 609.51 Å3
Hydrophobicity 0.194
Hydrophilicity 1.266
Buriedness 0.785
Don/acc character 1.574
SiteScore 1.208
D Score 0.999

Compound SPM
Residue . / 3128
Chain SC / 1
Non-redundant True
Interacting RNA chains B/1
Volume 743.97 Å3
Hydrophobicity 0.152
Hydrophilicity 1.509
Buriedness 0.857
Don/acc character 0.989
SiteScore 1.106
D Score 0.962

Compound SPM
Residue . / 3129
Chain TC / 1
Non-redundant True
Interacting RNA chains B/1
Volume 712.41 Å3
Hydrophobicity 0.199
Hydrophilicity 1.369
Buriedness 0.878
Don/acc character 1.623
SiteScore 1.270
D Score 1.020

Compound SPM
Residue . / 3130
Chain UC / 1
Non-redundant True
Interacting RNA chains B/1
Volume 789.24 Å3
Hydrophobicity 0.125
Hydrophilicity 1.316
Buriedness 0.779
Don/acc character 1.286
SiteScore 1.054
D Score 0.978

Compound SPM
Residue . / 3131
Chain VC / 1
Non-redundant True
Interacting RNA chains B/1
Volume 217.12 Å3
Hydrophobicity 0.070
Hydrophilicity 1.074
Buriedness 0.546
Don/acc character 2.500
SiteScore 0.878
D Score 0.699

Compound SPM
Residue . / 3132
Chain WC / 1
Non-redundant True
Interacting RNA chains B/1
Volume 920.96 Å3
Hydrophobicity 0.361
Hydrophilicity 1.116
Buriedness 0.852
Don/acc character 2.531
SiteScore 1.253
D Score 1.088

Compound SPM
Residue . / 3133
Chain XC / 1
Non-redundant True
Interacting RNA chains B/1
Volume 717.90 Å3
Hydrophobicity 0.154
Hydrophilicity 1.083
Buriedness 0.707
Don/acc character 1.245
SiteScore 1.156
D Score 1.011

Compound SPM
Residue . / 3134
Chain YC / 1
Non-redundant True
Interacting RNA chains B/1
Volume 721.33 Å3
Hydrophobicity 0.105
Hydrophilicity 1.469
Buriedness 0.848
Don/acc character 1.996
SiteScore 1.100
D Score 0.970

Compound SPM
Residue . / 3135
Chain ZC / 1
Non-redundant True
Interacting RNA chains B/1
Volume 890.77 Å3
Hydrophobicity 0.311
Hydrophilicity 1.230
Buriedness 0.847
Don/acc character 2.180
SiteScore 1.250
D Score 1.047

Compound SPM
Residue . / 3136
Chain AD / 1
Non-redundant True
Interacting RNA chains B/1
Volume 444.87 Å3
Hydrophobicity 0.146
Hydrophilicity 1.411
Buriedness 0.794
Don/acc character 1.510
SiteScore 1.214
D Score 0.956

Compound SPM
Residue . / 3137
Chain BD / 1
Non-redundant True
Interacting RNA chains B/1
Volume 466.14 Å3
Hydrophobicity 0.035
Hydrophilicity 1.185
Buriedness 0.710
Don/acc character 2.568
SiteScore 1.113
D Score 0.921

Compound SPM
Residue . / 3138
Chain CD / 1
Non-redundant True
Interacting RNA chains B/1
Volume 585.50 Å3
Hydrophobicity 0.265
Hydrophilicity 1.173
Buriedness 0.803
Don/acc character 1.258
SiteScore 1.220
D Score 1.040

Compound SPM
Residue . / 3139
Chain DD / 1
Non-redundant True
Interacting RNA chains B/1
Volume -
Hydrophobicity -
Hydrophilicity -
Buriedness -
Don/acc character -
SiteScore -
D Score -

Compound SPM
Residue . / 3140
Chain ED / 1
Non-redundant True
Interacting RNA chains B/1
Volume 219.86 Å3
Hydrophobicity 0.000
Hydrophilicity 1.345
Buriedness 0.696
Don/acc character 1.297
SiteScore 0.868
D Score 0.559

Compound SPM
Residue . / 3141
Chain FD / 1
Non-redundant True
Interacting RNA chains B/1
Volume 191.05 Å3
Hydrophobicity 0.121
Hydrophilicity 0.965
Buriedness 0.639
Don/acc character 4.695
SiteScore 0.813
D Score 0.609

Compound SPM
Residue . / 3142
Chain GD / 1
Non-redundant True
Interacting RNA chains B/1
Volume 155.38 Å3
Hydrophobicity 0.136
Hydrophilicity 0.922
Buriedness 0.536
Don/acc character 2.462
SiteScore 0.820
D Score 0.840

Compound SPM
Residue . / 3143
Chain HD / 1
Non-redundant True
Interacting RNA chains B/1
Volume 335.45 Å3
Hydrophobicity 1.034
Hydrophilicity 1.112
Buriedness 0.863
Don/acc character 1.400
SiteScore 0.986
D Score 0.936

Compound SPM
Residue . / 3144
Chain ID / 1
Non-redundant True
Interacting RNA chains B/1
Volume 340.60 Å3
Hydrophobicity 0.241
Hydrophilicity 1.050
Buriedness 0.718
Don/acc character 2.654
SiteScore 1.014
D Score 1.029

Compound SPM
Residue . / 3001
Chain XJ / 4
Non-redundant True
Interacting RNA chains C/4
Volume 396.85 Å3
Hydrophobicity 0.059
Hydrophilicity 1.444
Buriedness 0.881
Don/acc character 0.778
SiteScore 1.089
D Score 0.955

Compound SPM
Residue . / 3002
Chain YJ / 4
Non-redundant True
Interacting RNA chains C/4
Volume 741.91 Å3
Hydrophobicity 0.243
Hydrophilicity 1.072
Buriedness 0.795
Don/acc character 1.803
SiteScore 1.215
D Score 1.068

Compound SPM
Residue . / 3003
Chain ZJ / 4
Non-redundant True
Interacting RNA chains C/4
Volume 781.01 Å3
Hydrophobicity 0.106
Hydrophilicity 1.372
Buriedness 0.807
Don/acc character 1.963
SiteScore 1.223
D Score 0.977

Compound SPM
Residue . / 3004
Chain AK / 4
Non-redundant True
Interacting RNA chains C/4
Volume -
Hydrophobicity -
Hydrophilicity -
Buriedness -
Don/acc character -
SiteScore -
D Score -

Compound SPM
Residue . / 3005
Chain BK / 4
Non-redundant True
Interacting RNA chains C/4
Volume 355.35 Å3
Hydrophobicity 0.095
Hydrophilicity 1.248
Buriedness 0.776
Don/acc character 1.764
SiteScore 0.857
D Score 0.556

Compound SPM
Residue . / 3006
Chain CK / 4
Non-redundant True
Interacting RNA chains C/4
Volume 279.55 Å3
Hydrophobicity 0.102
Hydrophilicity 1.285
Buriedness 0.745
Don/acc character 1.082
SiteScore 1.140
D Score 0.915

Compound SPM
Residue . / 3007
Chain DK / 4
Non-redundant True
Interacting RNA chains C/4
Volume 339.57 Å3
Hydrophobicity 0.137
Hydrophilicity 0.998
Buriedness 0.706
Don/acc character 4.940
SiteScore 1.090
D Score 0.944

Compound SPM
Residue . / 3008
Chain EK / 4
Non-redundant True
Interacting RNA chains C/4
Volume 713.10 Å3
Hydrophobicity 0.077
Hydrophilicity 1.339
Buriedness 0.730
Don/acc character 1.328
SiteScore 1.134
D Score 0.893

Compound SPM
Residue . / 3009
Chain FK / 4
Non-redundant True
Interacting RNA chains C/4
Volume 661.99 Å3
Hydrophobicity 0.117
Hydrophilicity 1.350
Buriedness 0.753
Don/acc character 1.167
SiteScore 1.186
D Score 0.951

Compound SPM
Residue . / 3010
Chain GK / 4
Non-redundant True
Interacting RNA chains C/4
Volume 645.18 Å3
Hydrophobicity 0.094
Hydrophilicity 1.593
Buriedness 0.834
Don/acc character 1.436
SiteScore 1.091
D Score 0.921

Compound SPM
Residue . / 3011
Chain HK / 4
Non-redundant True
Interacting RNA chains C/4
Volume 157.78 Å3
Hydrophobicity 0.020
Hydrophilicity 0.858
Buriedness 0.690
Don/acc character 4.228
SiteScore 0.640
D Score 0.383

Compound SPM
Residue . / 3012
Chain IK / 4
Non-redundant True
Interacting RNA chains C/4
Volume 564.58 Å3
Hydrophobicity 0.208
Hydrophilicity 1.111
Buriedness 0.784
Don/acc character 2.156
SiteScore 1.154
D Score 0.980

Compound SPM
Residue . / 3013
Chain JK / 4
Non-redundant True
Interacting RNA chains C/4
Volume 417.43 Å3
Hydrophobicity 0.036
Hydrophilicity 1.077
Buriedness 0.713
Don/acc character 1.846
SiteScore 0.910
D Score 0.693

Compound SPM
Residue . / 3014
Chain KK / 4
Non-redundant True
Interacting RNA chains C/4
Volume 215.75 Å3
Hydrophobicity 0.000
Hydrophilicity 1.325
Buriedness 0.854
Don/acc character 1.487
SiteScore 0.709
D Score 0.501

Compound SPM
Residue . / 3015
Chain LK / 4
Non-redundant True
Interacting RNA chains C/4
Volume 349.17 Å3
Hydrophobicity 0.409
Hydrophilicity 0.976
Buriedness 0.786
Don/acc character 2.504
SiteScore 1.210
D Score 1.079

Compound SPM
Residue . / 3016
Chain MK / 4
Non-redundant True
Interacting RNA chains C/4
Volume 842.07 Å3
Hydrophobicity 0.411
Hydrophilicity 1.306
Buriedness 0.866
Don/acc character 1.560
SiteScore 1.262
D Score 1.034

Compound SPM
Residue . / 3017
Chain NK / 4
Non-redundant True
Interacting RNA chains C/4
Volume 324.14 Å3
Hydrophobicity 0.059
Hydrophilicity 1.105
Buriedness 0.642
Don/acc character 1.391
SiteScore 1.105
D Score 0.956

Compound SPM
Residue . / 3018
Chain OK / 4
Non-redundant True
Interacting RNA chains C/4
Volume 655.47 Å3
Hydrophobicity 0.283
Hydrophilicity 0.935
Buriedness 0.724
Don/acc character 3.187
SiteScore 1.188
D Score 1.069

Compound SPM
Residue . / 201
Chain QN / AL
Non-redundant True
Interacting RNA chains B/1
Volume -
Hydrophobicity -
Hydrophilicity -
Buriedness -
Don/acc character -
SiteScore -
D Score -

Compound SPM
Residue . / 101
Chain WN / Ah
Non-redundant True
Interacting RNA chains B/1
Volume 268.23 Å3
Hydrophobicity 0.186
Hydrophilicity 1.296
Buriedness 0.816
Don/acc character 1.814
SiteScore 0.815
D Score 0.669