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 % 106 270 38
95 % 106 271 53 Flexibility: Low
Max RMSD: 2.0, Avg RMSD: 1.1
PDBFlex
90 % 106 271 58
70 % 106 271 70
50 % 135 432 28
40 % 135 432 41
30 % 150 545 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 % 106 272 36
95 % 106 272 49 Flexibility: Low
Max RMSD: 1.9, Avg RMSD: 0.7
PDBFlex
90 % 106 272 54
70 % 106 272 66
50 % 129 426 35
40 % 146 557 19
30 % 146 557 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 % 65 218 54
95 % 106 279 39 Flexibility: Low
Max RMSD: 1.2, Avg RMSD: 0.7
PDBFlex
90 % 106 279 45
70 % 129 430 21
50 % 129 443 26
40 % 129 443 39
30 % 129 443 58
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 % 106 273 34
95 % 106 273 47 Flexibility: Low
Max RMSD: 2.4, Avg RMSD: 0.7
PDBFlex
90 % 106 273 52
70 % 106 273 63
50 % 132 430 34
40 % 132 430 46
30 % 147 546 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 % 106 271 37
95 % 106 271 55 Flexibility: Low
Max RMSD: 2.1, Avg RMSD: 0.9
PDBFlex
90 % 106 271 60
70 % 106 284 54
50 % 106 284 93
40 % 106 284 116
30 % 106 284 126
Entity #15 | Chains: O
30S ribosomal protein S15 protein, length: 89 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 106 275 31
95 % 110 280 38
90 % 110 280 44
70 % 110 280 56
50 % 136 439 27
40 % 136 444 37
30 % 136 444 57
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 % 106 267 41
95 % 106 272 51 Flexibility: No
Max RMSD: 1.3, Avg RMSD: 0.4
PDBFlex
90 % 106 272 56
70 % 106 272 68
50 % 106 282 94
40 % 106 282 117
30 % 132 423 65
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 87 284
95 % 106 266 56 Flexibility: Low
Max RMSD: 1.9, Avg RMSD: 0.6
PDBFlex
90 % 106 270 61
70 % 106 270 71
50 % 106 270 98
40 % 106 270 121
30 % 106 270 129
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 51 741
95 % 96 237 69 Flexibility: Low
Max RMSD: 3.4, Avg RMSD: 0.8
PDBFlex
90 % 96 237 71
70 % 96 237 86
50 % 96 237 117
40 % 96 237 141
30 % 96 237 146
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 % 107 275 30
95 % 107 275 43 Flexibility: Low
Max RMSD: 3.7, Avg RMSD: 0.9
PDBFlex
90 % 107 275 49
70 % 107 275 60
50 % 130 432 30
40 % 130 435 42
30 % 130 435 59
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 % 106 272 32
95 % 106 273 44 Flexibility: Low
Max RMSD: 9.2, Avg RMSD: 1.5
PDBFlex
90 % 106 273 50
70 % 106 273 61
50 % 129 419 37
40 % 129 424 47
30 % 129 424 64
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 51 545
95 % 106 271 52 Flexibility: Low
Max RMSD: 1.4, Avg RMSD: 0.7
PDBFlex
90 % 106 271 57
70 % 106 271 69
50 % 106 271 97
40 % 106 271 119
30 % 106 271 128
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 % 106 262 43
95 % 106 262 59 Flexibility: Low
Max RMSD: 1.2, Avg RMSD: 0.5
PDBFlex
90 % 106 262 63
70 % 106 262 76
50 % 106 262 104
40 % 106 262 127
30 % 106 262 134
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 % 95 236 49
95 % 95 236 70 Flexibility: Low
Max RMSD: 1.5, Avg RMSD: 0.7
PDBFlex
90 % 95 236 72
70 % 95 236 87
50 % 99 310 86
40 % 99 310 106
30 % 99 310 120
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 % 105 265 42
95 % 106 273 45 Flexibility: Low
Max RMSD: 1.6, Avg RMSD: 0.5
PDBFlex
90 % 106 273 51
70 % 106 273 62
50 % 129 427 32
40 % 129 432 43
30 % 129 432 60
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 % 106 272 35
95 % 106 272 48 Flexibility: Low
Max RMSD: 4.8, Avg RMSD: 0.6
PDBFlex
90 % 106 272 53
70 % 106 272 64
50 % 130 427 33
40 % 130 427 45
30 % 130 429 63
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 % 108 277 28
95 % 114 283 37 Flexibility: Low
Max RMSD: 2.8, Avg RMSD: 0.8
PDBFlex
90 % 114 283 42
70 % 114 283 52
50 % 114 283 92
40 % 114 283 115
30 % 135 366 95
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 % 107 276 29
95 % 107 277 40 Flexibility: Low
Max RMSD: 2.2, Avg RMSD: 0.8
PDBFlex
90 % 107 277 46
70 % 107 277 57
50 % 130 367 67
40 % 130 372 85
30 % 130 372 97
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 % 107 272 33
95 % 107 272 46 Flexibility: No
Max RMSD: 1.3, Avg RMSD: 0.4
PDBFlex
90 % 107 276 47
70 % 107 276 58
50 % 132 432 29
40 % 133 438 40
30 % 150 562 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 91 233
95 % 106 272 50
90 % 106 272 55
70 % 106 272 67
50 % 129 421 36
40 % 129 421 48
30 % 144 546 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