3T1Y

Structure of the Thermus thermophilus 30S ribosomal subunit complexed with a human anti-codon stem loop (HASL) of transfer RNA Lysine 3 (TRNALYS3) bound to an mRNA with an AAG-codon in the A-site and paromomycin


Sequence Similarity Clusters for the Entities in PDB 3T1Y

Entity #1 | Chains: A
16S rRNA rna, length: 1513 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
Entity #10 | Chains: J
30S ribosomal protein S10 protein, length: 105 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name Structural variation in cluster
100 % 115 290 34
95 % 115 291 49 Flexibility: Low
Max RMSD: 2.0, Avg RMSD: 1.1
PDBFlex
90 % 115 291 54
70 % 115 291 65
50 % 144 455 25
40 % 144 455 40
30 % 159 572 34
Entity #11 | Chains: K
30S ribosomal protein S11 protein, length: 129 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name Structural variation in cluster
100 % 115 292 32
95 % 115 292 45 Flexibility: Low
Max RMSD: 1.9, Avg RMSD: 0.7
PDBFlex
90 % 115 292 50
70 % 115 292 60
50 % 138 449 33
40 % 155 584 19
30 % 155 584 33
Entity #12 | Chains: L
30S ribosomal protein S12 protein, length: 132 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name Structural variation in cluster
100 % 65 220 54
95 % 115 299 37 Flexibility: Low
Max RMSD: 1.2, Avg RMSD: 0.7
PDBFlex
90 % 115 299 41
70 % 138 453 17
50 % 138 466 24
40 % 138 466 38
30 % 138 466 57
Entity #13 | Chains: M
30S ribosomal protein S13 protein, length: 126 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name Structural variation in cluster
100 % 115 293 30
95 % 115 293 43 Flexibility: Low
Max RMSD: 2.4, Avg RMSD: 0.7
PDBFlex
90 % 115 293 47
70 % 115 293 58
50 % 141 453 32
40 % 141 453 46
30 % 156 573 37
Entity #14 | Chains: N
30S ribosomal protein S14 type Z protein, length: 61 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name Structural variation in cluster
100 % 115 291 33
95 % 115 291 50 Flexibility: Low
Max RMSD: 2.1, Avg RMSD: 0.9
PDBFlex
90 % 115 291 55
70 % 115 304 49
50 % 115 304 89
40 % 115 304 110
30 % 115 304 122
Entity #15 | Chains: O
30S ribosomal protein S15 protein, length: 89 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 115 295 27
95 % 119 300 36
90 % 119 300 40
70 % 119 300 50
50 % 145 461 26
40 % 145 466 37
30 % 145 466 56
Entity #16 | Chains: P
30S ribosomal protein S16 protein, length: 88 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name Structural variation in cluster
100 % 115 287 35
95 % 115 292 47 Flexibility: No
Max RMSD: 1.3, Avg RMSD: 0.4
PDBFlex
90 % 115 292 52
70 % 115 292 62
50 % 115 302 90
40 % 115 308 107
30 % 141 451 64
Entity #17 | Chains: Q
30S ribosomal protein S17 protein, length: 105 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name Structural variation in cluster
100 % 24 91 276
95 % 115 285 51 Flexibility: Low
Max RMSD: 1.9, Avg RMSD: 0.6
PDBFlex
90 % 115 289 56
70 % 115 289 66
50 % 115 289 94
40 % 115 289 117
30 % 115 289 127
Entity #18 | Chains: R
30S ribosomal protein S18 protein, length: 88 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name Structural variation in cluster
100 % 9 51 753
95 % 102 246 65 Flexibility: Low
Max RMSD: 3.4, Avg RMSD: 0.8
PDBFlex
90 % 102 246 68
70 % 102 246 84
50 % 102 246 113
40 % 102 246 138
30 % 102 246 143
Entity #19 | Chains: S
30S ribosomal protein S19 protein, length: 93 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name Structural variation in cluster
100 % 116 295 26
95 % 116 295 39 Flexibility: Low
Max RMSD: 3.7, Avg RMSD: 0.9
PDBFlex
90 % 116 295 44
70 % 116 295 54
50 % 139 455 28
40 % 139 458 42
30 % 139 458 58
Entity #2 | Chains: B
30S ribosomal protein S2 protein, length: 256 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name Structural variation in cluster
100 % 115 292 28
95 % 115 293 40 Flexibility: Low
Max RMSD: 9.2, Avg RMSD: 1.5
PDBFlex
90 % 115 293 45
70 % 115 293 55
50 % 138 441 35
40 % 138 447 47
30 % 138 447 63
Entity #20 | Chains: T
30S ribosomal protein S20 protein, length: 106 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name Structural variation in cluster
100 % 11 53 499
95 % 115 291 48 Flexibility: Low
Max RMSD: 1.4, Avg RMSD: 0.7
PDBFlex
90 % 115 291 53
70 % 115 291 64
50 % 115 291 93
40 % 115 291 116
30 % 115 291 126
Entity #21 | Chains: V
30S ribosomal protein Thx protein, length: 27 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name Structural variation in cluster
100 % 115 282 41
95 % 115 282 55 Flexibility: Low
Max RMSD: 1.2, Avg RMSD: 0.5
PDBFlex
90 % 115 282 61
70 % 115 282 71
50 % 115 282 98
40 % 115 282 121
30 % 115 282 129
Entity #22 | Chains: W
mRNA A-site fragment rna, length: 3 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
Entity #23 | Chains: X
tRNA ASL human Lys3 rna, length: 11 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
Entity #3 | Chains: C
30S ribosomal protein S3 protein, length: 239 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name Structural variation in cluster
100 % 101 245 46
95 % 101 245 66 Flexibility: Low
Max RMSD: 1.5, Avg RMSD: 0.7
PDBFlex
90 % 101 245 69
70 % 101 245 85
50 % 105 320 86
40 % 105 320 104
30 % 105 320 116
Entity #4 | Chains: D
30S ribosomal protein S4 protein, length: 209 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name Structural variation in cluster
100 % 114 285 38
95 % 115 293 41 Flexibility: Low
Max RMSD: 1.6, Avg RMSD: 0.5
PDBFlex
90 % 115 293 46
70 % 115 293 57
50 % 138 449 29
40 % 138 455 43
30 % 138 455 59
Entity #5 | Chains: E
30S ribosomal protein S5 protein, length: 162 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name Structural variation in cluster
100 % 115 292 31
95 % 115 292 44 Flexibility: Low
Max RMSD: 4.8, Avg RMSD: 0.6
PDBFlex
90 % 115 292 49
70 % 115 292 59
50 % 139 450 31
40 % 139 450 45
30 % 139 452 61
Entity #6 | Chains: F
30S ribosomal protein S6 protein, length: 101 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name Structural variation in cluster
100 % 117 297 24
95 % 123 303 35 Flexibility: Low
Max RMSD: 2.8, Avg RMSD: 0.8
PDBFlex
90 % 123 303 39
70 % 123 303 48
50 % 123 303 88
40 % 123 303 109
30 % 144 386 88
Entity #7 | Chains: G
30S ribosomal protein S7 protein, length: 156 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name Structural variation in cluster
100 % 116 296 25
95 % 116 297 38 Flexibility: Low
Max RMSD: 2.2, Avg RMSD: 0.8
PDBFlex
90 % 116 297 42
70 % 116 297 51
50 % 139 388 60
40 % 139 394 71
30 % 139 394 87
Entity #8 | Chains: H
30S ribosomal protein S8 protein, length: 138 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name Structural variation in cluster
100 % 116 292 29
95 % 116 292 42 Flexibility: No
Max RMSD: 1.3, Avg RMSD: 0.4
PDBFlex
90 % 116 296 43
70 % 116 296 52
50 % 141 454 27
40 % 142 461 39
30 % 159 589 32
Entity #9 | Chains: I
30S ribosomal protein S9 protein, length: 128 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 15 94 223
95 % 115 292 46
90 % 115 292 51
70 % 115 292 61
50 % 138 443 34
40 % 138 444 48
30 % 153 573 36

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