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 % 104 268 39
95 % 104 269 53 Flexibility: Low
Max RMSD: 2.1, Avg RMSD: 1.1
PDBFlex
90 % 104 269 58
70 % 104 269 68
50 % 133 419 26
40 % 133 419 38
30 % 148 525 31
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 % 104 270 35
95 % 104 270 49 Flexibility: Low
Max RMSD: 1.9, Avg RMSD: 0.7
PDBFlex
90 % 104 270 54
70 % 104 270 64
50 % 127 413 32
40 % 144 525 19
30 % 144 525 32
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 % 64 217 51
95 % 104 277 40 Flexibility: Low
Max RMSD: 1.2, Avg RMSD: 0.7
PDBFlex
90 % 104 277 45
70 % 127 420 19
50 % 127 430 24
40 % 127 430 36
30 % 127 430 55
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 % 104 271 33
95 % 104 271 47 Flexibility: Low
Max RMSD: 2.4, Avg RMSD: 0.7
PDBFlex
90 % 104 271 52
70 % 104 271 62
50 % 130 417 31
40 % 130 417 46
30 % 145 523 34
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 % 104 269 38
95 % 104 269 54 Flexibility: Low
Max RMSD: 2.1, Avg RMSD: 0.8
PDBFlex
90 % 104 269 59
70 % 104 277 55
50 % 104 277 91
40 % 104 277 115
30 % 104 277 123
Entity #15 | Chains: O
30S ribosomal protein S15 protein, length: 89 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name Structural variation in cluster
100 % 104 273 30
95 % 108 278 38 Flexibility: Low
Max RMSD: 1.3, Avg RMSD: 0.6
PDBFlex
90 % 108 278 43
70 % 108 278 53
50 % 134 426 25
40 % 134 431 35
30 % 134 431 54
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 % 104 265 41
95 % 104 270 51 Flexibility: No
Max RMSD: 1.3, Avg RMSD: 0.5
PDBFlex
90 % 104 270 56
70 % 104 270 66
50 % 104 277 90
40 % 104 277 114
30 % 130 412 63
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 87 254
95 % 104 264 56 Flexibility: Low
Max RMSD: 1.9, Avg RMSD: 0.6
PDBFlex
90 % 104 268 60
70 % 104 268 69
50 % 104 268 94
40 % 104 268 118
30 % 104 268 128
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 51 715
95 % 94 235 65 Flexibility: Low
Max RMSD: 8.4, Avg RMSD: 0.9
PDBFlex
90 % 94 235 70
70 % 94 235 82
50 % 94 235 111
40 % 94 235 135
30 % 94 235 143
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 % 105 273 29
95 % 105 273 42 Flexibility: Low
Max RMSD: 3.7, Avg RMSD: 0.9
PDBFlex
90 % 105 273 48
70 % 105 273 59
50 % 128 419 28
40 % 128 422 40
30 % 128 422 56
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 % 104 270 31
95 % 104 271 44 Flexibility: Low
Max RMSD: 9.2, Avg RMSD: 1.5
PDBFlex
90 % 104 271 50
70 % 104 271 60
50 % 127 408 36
40 % 127 413 45
30 % 127 413 62
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 51 516
95 % 104 269 52 Flexibility: Low
Max RMSD: 1.4, Avg RMSD: 0.7
PDBFlex
90 % 104 269 57
70 % 104 269 67
50 % 104 269 93
40 % 104 269 116
30 % 104 269 127
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 % 104 260 43
95 % 104 260 59 Flexibility: Low
Max RMSD: 1.2, Avg RMSD: 0.5
PDBFlex
90 % 104 260 63
70 % 104 260 74
50 % 104 260 98
40 % 104 260 121
30 % 104 260 133
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 % 93 234 48
95 % 93 234 66 Flexibility: Low
Max RMSD: 1.5, Avg RMSD: 0.7
PDBFlex
90 % 93 234 71
70 % 93 234 83
50 % 97 308 84
40 % 97 308 103
30 % 97 308 116
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 % 103 263 42
95 % 104 271 45 Flexibility: Low
Max RMSD: 1.6, Avg RMSD: 0.6
PDBFlex
90 % 104 271 51
70 % 104 271 61
50 % 127 414 30
40 % 127 419 41
30 % 127 419 57
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 % 104 270 34
95 % 104 270 48 Flexibility: Low
Max RMSD: 4.8, Avg RMSD: 0.6
PDBFlex
90 % 104 270 53
70 % 104 270 63
50 % 128 416 29
40 % 128 416 42
30 % 128 418 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 % 106 275 27
95 % 112 281 37 Flexibility: Low
Max RMSD: 2.9, Avg RMSD: 0.9
PDBFlex
90 % 112 281 42
70 % 112 281 51
50 % 112 281 88
40 % 112 281 110
30 % 133 353 93
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 % 105 274 28
95 % 105 275 41 Flexibility: Low
Max RMSD: 4.2, Avg RMSD: 0.8
PDBFlex
90 % 105 275 46
70 % 105 275 56
50 % 128 354 68
40 % 128 359 85
30 % 128 359 95
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 % 105 270 32
95 % 105 270 46 Flexibility: No
Max RMSD: 1.3, Avg RMSD: 0.4
PDBFlex
90 % 105 274 47
70 % 105 274 57
50 % 130 419 27
40 % 131 425 37
30 % 148 538 30
Entity #9 | Chains: I
30S ribosomal protein S9 protein, length: 128 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name Structural variation in cluster
100 % 15 91 217
95 % 104 270 50 Flexibility: Low
Max RMSD: 1.5, Avg RMSD: 0.8
PDBFlex
90 % 104 270 55
70 % 104 270 65
50 % 127 410 35
40 % 127 410 48
30 % 142 520 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.