5J4D

E. coli release factor 1 bound to the 70S ribosome in response to a pseudouridylated stop codon


Sequence Similarity Clusters for the Entities in PDB 5J4D

Entity #1 | Chains: A,FB
16S ribosomal RNA rna, length: 1507 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
Entity #10 | Chains: J,OB
50S ribosomal protein L9 protein, length: 148 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 1 18 1557
95 % 72 165 126
90 % 72 165 131
70 % 72 165 140
50 % 72 170 161
40 % 97 349 98
30 % 97 362 96
Entity #11 | Chains: K,PB
50S ribosomal protein L13 protein, length: 140 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 81 195 73
95 % 81 196 101
90 % 81 196 107
70 % 81 196 118
50 % 82 201 128
40 % 108 434 70
30 % 108 434 75
Entity #12 | Chains: L,QB
50S ribosomal protein L14 protein, length: 122 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 1 25 1218
95 % 81 199 95
90 % 81 199 101
70 % 85 273 80
50 % 111 474 44
40 % 111 474 49
30 % 111 474 52
Entity #13 | Chains: M,RB
50S ribosomal protein L15 protein, length: 150 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 81 199 69
95 % 81 199 96
90 % 81 199 104
70 % 81 199 111
50 % 81 240 113
40 % 110 456 60
30 % 110 456 62
Entity #14 | Chains: N,SB
50S ribosomal protein L16 protein, length: 141 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 1 17 1625
95 % 81 200 87
90 % 81 200 93
70 % 84 227 92
50 % 110 459 49
40 % 110 459 58
30 % 110 459 60
Entity #15 | Chains: O,TB
50S ribosomal protein L17 protein, length: 118 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 82 204 54
95 % 82 204 79
90 % 82 204 84
70 % 82 204 97
50 % 111 420 58
40 % 111 458 53
30 % 111 460 55
Entity #16 | Chains: P,UB
50S ribosomal protein L18 protein, length: 112 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 81 184 83
95 % 81 184 111
90 % 81 184 118
70 % 81 184 127
50 % 110 441 57
40 % 110 441 72
30 % 110 441 77
Entity #17 | Chains: Q,VB
50S ribosomal protein L19 protein, length: 146 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 1 17 1595
95 % 81 197 100
90 % 81 197 106
70 % 77 189 125
50 % 77 189 146
40 % 77 189 161
30 % 77 189 162
Entity #18 | Chains: R,WB
50S ribosomal protein L20 protein, length: 118 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 81 194 75
95 % 81 199 98
90 % 81 199 103
70 % 81 199 113
50 % 111 461 46
40 % 111 469 51
30 % 111 469 53
Entity #19 | Chains: S,XB
50S ribosomal protein L21 protein, length: 101 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 81 199 62
95 % 81 199 90
90 % 81 199 96
70 % 81 199 107
50 % 84 258 105
40 % 110 456 61
30 % 110 456 63
Entity #2 | Chains: B,GB
25S ribosomal RNA rna, length: 2880 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
Entity #20 | Chains: T,YB
50S ribosomal protein L22 protein, length: 113 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 82 207 58
95 % 83 208 80
90 % 83 208 85
70 % 83 208 98
50 % 109 430 59
40 % 109 430 73
30 % 109 430 78
Entity #21 | Chains: U,ZB
50S ribosomal protein L23 protein, length: 96 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 81 200 61
95 % 81 200 88
90 % 81 200 94
70 % 81 200 105
50 % 84 226 120
40 % 110 462 56
30 % 110 462 58
Entity #22 | Chains: AC,V
50S ribosomal protein L24 protein, length: 110 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 81 199 64
95 % 81 199 91
90 % 81 199 102
70 % 81 199 112
50 % 107 434 56
40 % 107 434 71
30 % 107 436 76
Entity #23 | Chains: BC,W
50S ribosomal protein L25 protein, length: 206 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 82 199 72
95 % 83 200 86
90 % 83 200 92
70 % 83 200 104
50 % 83 200 132
40 % 83 200 150
30 % 83 212 150
Entity #24 | Chains: CC,X
50S ribosomal protein L27 protein, length: 85 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 78 181 87
95 % 82 200 83
90 % 82 200 88
70 % 82 200 101
50 % 112 454 51
40 % 112 454 62
30 % 112 454 64
Entity #25 | Chains: DC,Y
50S ribosomal protein L28 protein, length: 98 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 1 21 1225
95 % 81 191 102
90 % 81 191 109
70 % 81 191 119
50 % 81 191 139
40 % 81 191 156
30 % 81 191 159
Entity #26 | Chains: EC,Z
50S ribosomal protein L29 protein, length: 72 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 81 184 79
95 % 81 192 106
90 % 81 192 114
70 % 81 192 123
50 % 81 192 143
40 % 107 388 87
30 % 110 414 83
Entity #27 | Chains: AA,FC
50S ribosomal protein L30 protein, length: 60 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 82 206 57
95 % 82 206 81
90 % 82 206 86
70 % 82 206 99
50 % 82 206 127
40 % 111 451 65
30 % 111 451 68
Entity #28 | Chains: BA,GC
50S ribosomal protein L31 protein, length: 71 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 81 182 92
95 % 81 182 116
90 % 81 182 125
70 % 81 182 134
50 % 81 198 148
40 % 81 275 126
30 % 81 276 136
Entity #29 | Chains: CA,HC
50S ribosomal protein L32 protein, length: 60 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 1 11 3058
95 % 81 194 103
90 % 81 194 111
70 % 81 194 120
50 % 84 228 121
40 % 84 228 140
30 % 110 448 72
Entity #3 | Chains: C,HB
5S ribosomal RNA rna, length: 120 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
Entity #30 | Chains: DA,IC
50S ribosomal protein L33 protein, length: 54 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 66 179 90
95 % 66 180 115
90 % 66 180 124
70 % 66 180 131
50 % 66 204 144
40 % 95 417 79
30 % 95 417 86
Entity #31 | Chains: EA,JC
50S ribosomal protein L34 protein, length: 49 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 81 199 66
95 % 81 199 93
90 % 81 199 98
70 % 81 199 109
50 % 110 455 52
40 % 110 455 63
30 % 110 455 65
Entity #32 | Chains: FA,KC
50S ribosomal protein L35 protein, length: 65 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 82 200 70
95 % 82 200 99
90 % 82 200 105
70 % 82 200 114
50 % 85 228 119
40 % 111 444 67
30 % 111 444 71
Entity #33 | Chains: GA,LC
50S ribosomal protein L36 protein, length: 37 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 53 147 110
95 % 53 147 142
90 % 53 147 149
70 % 55 209 132
50 % 80 395 79
40 % 80 395 95
30 % 80 395 94
Entity #34 | Chains: HA,MC
mRNA rna, length: 27 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
Entity #35 | Chains: JA,OC
Peptide chain release factor 1 protein, length: 368 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 1 5 8912
95 % 1 9 4611
90 % 1 9 4689
70 % 1 9 4729
50 % 1 9 4520
40 % 3 15 2799
30 % 3 15 2766
Entity #36 | Chains: KA,PC
30S ribosomal protein S2 protein, length: 256 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 150 332 30
95 % 150 334 47
90 % 150 334 52
70 % 150 334 61
50 % 176 530 29
40 % 176 536 34
30 % 176 536 38
Entity #37 | Chains: LA,QC
30S ribosomal protein S3 protein, length: 239 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 128 277 49
95 % 128 277 72
90 % 128 277 77
70 % 128 277 85
50 % 132 357 86
40 % 132 357 102
30 % 132 357 103
Entity #38 | Chains: MA,RC
30S ribosomal protein S4 protein, length: 209 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 149 326 36
95 % 150 334 46
90 % 150 334 51
70 % 150 334 60
50 % 176 515 31
40 % 176 544 30
30 % 176 544 35
Entity #39 | Chains: NA,SC
30S ribosomal protein S5 protein, length: 162 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 150 333 32
95 % 150 333 50
90 % 150 333 54
70 % 150 333 63
50 % 177 534 27
40 % 177 534 36
30 % 177 534 40
Entity #4 | Chains: D,IA,IB,NC
tRNA rna, length: 77 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
Entity #40 | Chains: OA,TC
30S ribosomal protein S6 protein, length: 101 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 152 338 25
95 % 158 344 38
90 % 158 344 43
70 % 158 344 52
50 % 158 344 89
40 % 158 344 104
30 % 159 371 97
Entity #41 | Chains: PA,UC
30S ribosomal protein S7 protein, length: 156 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 151 337 26
95 % 151 338 45
90 % 151 338 50
70 % 151 336 59
50 % 178 471 54
40 % 178 477 66
30 % 178 477 69
Entity #42 | Chains: QA,VC
30S ribosomal protein S8 protein, length: 138 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 150 333 28
95 % 150 333 49
90 % 151 337 49
70 % 151 337 57
50 % 179 543 22
40 % 179 549 28
30 % 200 739 23
Entity #43 | Chains: RA,WC
30S ribosomal protein S9 protein, length: 128 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 22 101 238
95 % 150 333 51
90 % 150 333 55
70 % 150 333 64
50 % 176 527 30
40 % 176 527 38
30 % 176 527 42
Entity #44 | Chains: SA,XC
30S ribosomal protein S10 protein, length: 105 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 150 331 34
95 % 150 332 54
90 % 150 332 58
70 % 150 332 67
50 % 177 538 24
40 % 177 538 32
30 % 177 571 31
Entity #45 | Chains: TA,YC
30S ribosomal protein S11 protein, length: 129 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 150 333 31
95 % 150 333 52
90 % 150 333 56
70 % 150 333 65
50 % 176 533 28
40 % 176 533 37
30 % 176 533 41
Entity #46 | Chains: UA,ZC
30S ribosomal protein S12 protein, length: 132 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 20 32 706
95 % 150 340 44
90 % 150 340 48
70 % 177 537 15
50 % 177 554 20
40 % 177 554 27
30 % 177 554 33
Entity #47 | Chains: AD,VA
30S ribosomal protein S13 protein, length: 126 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 150 334 29
95 % 150 334 48
90 % 150 334 53
70 % 150 334 62
50 % 179 538 26
40 % 179 541 33
30 % 179 541 37
Entity #48 | Chains: BD,WA
30S ribosomal protein S14 type Z protein, length: 61 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 150 332 33
95 % 150 332 55
90 % 150 332 59
70 % 150 339 56
50 % 150 352 87
40 % 150 352 103
30 % 150 352 105
Entity #49 | Chains: CD,XA
30S ribosomal protein S15 protein, length: 89 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 150 336 27
95 % 154 341 43
90 % 154 341 46
70 % 154 341 55
50 % 183 550 21
40 % 183 550 29
30 % 183 550 34
Entity #5 | Chains: E,JB
50S ribosomal protein L2 protein, length: 275 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 82 200 67
95 % 82 200 97
90 % 82 200 99
70 % 85 224 93
50 % 111 461 48
40 % 111 461 57
30 % 111 461 59
Entity #50 | Chains: DD,YA
30S ribosomal protein S16 protein, length: 88 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 150 328 35
95 % 150 333 53
90 % 150 333 57
70 % 150 333 66
50 % 150 333 92
40 % 150 333 107
30 % 150 333 109
Entity #51 | Chains: ED,ZA
30S ribosomal protein S17 protein, length: 105 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 35 101 308
95 % 149 326 57
90 % 150 330 61
70 % 150 330 69
50 % 150 330 94
40 % 150 330 110
30 % 150 330 112
Entity #52 | Chains: AB,FD
30S ribosomal protein S18 protein, length: 88 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 115 223 59
95 % 129 277 71
90 % 129 277 76
70 % 129 277 84
50 % 129 277 109
40 % 129 277 128
30 % 129 277 138
Entity #53 | Chains: BB,GD
30S ribosomal protein S19 protein, length: 93 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 134 291 45
95 % 134 291 64
90 % 134 291 71
70 % 151 336 58
50 % 177 540 23
40 % 177 540 31
30 % 177 540 36
Entity #54 | Chains: CB,HD
30S ribosomal protein S20 protein, length: 106 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 13 56 547
95 % 150 332 56
90 % 150 332 60
70 % 150 332 68
50 % 150 332 93
40 % 150 332 108
30 % 150 332 110
Entity #55 | Chains: DB,ID
30S ribosomal protein Thx protein, length: 27 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 136 290 46
95 % 136 290 66
90 % 136 290 73
70 % 136 290 82
50 % 136 290 104
40 % 136 290 124
30 % 136 290 131
Entity #6 | Chains: F,KB
50S ribosomal protein L3 protein, length: 206 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 81 199 65
95 % 81 199 92
90 % 81 199 97
70 % 81 199 108
50 % 117 467 47
40 % 117 471 54
30 % 117 472 56
Entity #7 | Chains: G,LB
50S ribosomal protein L4 protein, length: 205 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 1 16 1732
95 % 82 200 94
90 % 82 200 100
70 % 82 200 110
50 % 85 229 118
40 % 85 239 134
30 % 112 453 67
Entity #8 | Chains: H,MB
50S ribosomal protein L5 protein, length: 182 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 1 17 1604
95 % 84 202 82
90 % 84 202 87
70 % 87 226 91
50 % 117 456 50
40 % 117 456 59
30 % 117 456 61
Entity #9 | Chains: I,NB
50S ribosomal protein L6 protein, length: 180 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 81 199 63
95 % 81 199 89
90 % 81 199 95
70 % 81 199 106
50 % 84 231 115
40 % 111 462 55
30 % 111 462 57

Instructions

In the table for each entity, view a list of similar sequences by selecting the link associated with the percentage cutoff.



View more detailed documentation on the redundancy reduction and sequence clustering procedure used by RCSB PDB.

You can also use the structure comparison tool to compare any 2 given structures