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 57
70 % 106 271 69
50 % 135 432 26
40 % 135 432 40
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 35
95 % 106 272 49 Flexibility: Low
Max RMSD: 1.9, Avg RMSD: 0.7
PDBFlex
90 % 106 272 53
70 % 106 272 65
50 % 129 426 33
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 44
70 % 129 430 18
50 % 129 443 24
40 % 129 443 38
30 % 129 443 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 % 106 273 33
95 % 106 273 47 Flexibility: Low
Max RMSD: 2.4, Avg RMSD: 0.7
PDBFlex
90 % 106 273 51
70 % 106 273 62
50 % 132 430 32
40 % 132 430 45
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 36
95 % 106 271 55 Flexibility: Low
Max RMSD: 2.1, Avg RMSD: 0.9
PDBFlex
90 % 106 271 59
70 % 106 284 54
50 % 106 284 92
40 % 106 284 115
30 % 106 284 124
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 30
95 % 110 280 38
90 % 110 280 43
70 % 110 280 55
50 % 136 439 25
40 % 136 444 37
30 % 136 444 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 % 106 267 41
95 % 106 272 51 Flexibility: No
Max RMSD: 1.3, Avg RMSD: 0.4
PDBFlex
90 % 106 272 55
70 % 106 272 67
50 % 106 282 93
40 % 106 282 116
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 87 267
95 % 106 266 56 Flexibility: Low
Max RMSD: 1.9, Avg RMSD: 0.6
PDBFlex
90 % 106 270 60
70 % 106 270 70
50 % 106 270 97
40 % 106 270 120
30 % 106 270 128
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 51 737
95 % 96 237 66 Flexibility: Low
Max RMSD: 3.4, Avg RMSD: 0.8
PDBFlex
90 % 96 237 70
70 % 96 237 84
50 % 96 237 117
40 % 96 237 140
30 % 96 237 145
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 29
95 % 107 275 43 Flexibility: Low
Max RMSD: 3.7, Avg RMSD: 0.9
PDBFlex
90 % 107 275 48
70 % 107 275 59
50 % 130 432 29
40 % 130 435 41
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 31
95 % 106 273 44 Flexibility: Low
Max RMSD: 9.2, Avg RMSD: 1.5
PDBFlex
90 % 106 273 49
70 % 106 273 60
50 % 129 419 35
40 % 129 424 46
30 % 129 424 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 51 540
95 % 106 271 52 Flexibility: Low
Max RMSD: 1.4, Avg RMSD: 0.7
PDBFlex
90 % 106 271 56
70 % 106 271 68
50 % 106 271 96
40 % 106 271 119
30 % 106 271 127
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 75
50 % 106 262 102
40 % 106 262 125
30 % 106 262 133
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 67 Flexibility: Low
Max RMSD: 1.5, Avg RMSD: 0.7
PDBFlex
90 % 95 236 71
70 % 95 236 85
50 % 99 310 86
40 % 99 310 106
30 % 99 310 118
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 50
70 % 106 273 61
50 % 129 427 30
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 34
95 % 106 272 48 Flexibility: Low
Max RMSD: 4.8, Avg RMSD: 0.6
PDBFlex
90 % 106 272 52
70 % 106 272 63
50 % 130 427 31
40 % 130 427 44
30 % 130 429 62
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 27
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 91
40 % 114 283 114
30 % 135 366 94
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 28
95 % 107 277 40 Flexibility: Low
Max RMSD: 2.2, Avg RMSD: 0.8
PDBFlex
90 % 107 277 45
70 % 107 277 56
50 % 130 367 66
40 % 130 372 84
30 % 130 372 96
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 32
95 % 107 272 46 Flexibility: No
Max RMSD: 1.3, Avg RMSD: 0.4
PDBFlex
90 % 107 276 46
70 % 107 276 57
50 % 132 432 28
40 % 133 438 39
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 91 229
95 % 106 272 50
90 % 106 272 54
70 % 106 272 66
50 % 129 421 34
40 % 129 421 47
30 % 144 546 35

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