1N33

Structure of the Thermus thermophilus 30S ribosomal subunit bound to codon and near-cognate transfer rna anticodon stem-loop mismatched at the second codon position at the a site with paromomycin


Sequence Similarity Clusters for the Entities in PDB 1N33

Entity #1 | Chains: A
16S RIBOSOMAL RNA rna, length: 1522 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
Entity #10 | 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 % 179 271 32
95 % 179 271 46 Flexibility: No
Max RMSD: 1.3, Avg RMSD: 0.4
PDBFlex
90 % 180 275 47
70 % 180 275 58
50 % 210 431 27
40 % 211 437 38
30 % 240 555 31
Entity #11 | 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 % 47 91 227
95 % 179 271 51 Flexibility: Low
Max RMSD: 1.5, Avg RMSD: 0.8
PDBFlex
90 % 179 271 55
70 % 179 271 66
50 % 207 420 33
40 % 207 420 47
30 % 234 539 35
Entity #12 | Chains: J
30S RIBOSOMAL PROTEIN S10 protein, length: 104 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 178 269 40
95 % 179 270 54
90 % 179 270 58
70 % 179 270 69
50 % 213 431 26
40 % 213 431 39
30 % 240 539 33
Entity #13 | Chains: K
30S RIBOSOMAL PROTEIN S11 protein, length: 129 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 179 271 36
95 % 179 271 50
90 % 179 271 54
70 % 179 271 65
50 % 207 425 32
40 % 236 550 19
30 % 236 550 32
Entity #14 | Chains: L
30S RIBOSOMAL PROTEIN S12 protein, length: 135 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name Structural variation in cluster
100 % 120 217 54
95 % 179 278 39 Flexibility: Low
Max RMSD: 1.2, Avg RMSD: 0.7
PDBFlex
90 % 179 278 44
70 % 207 429 18
50 % 207 442 24
40 % 207 442 37
30 % 207 442 57
Entity #15 | 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 % 179 272 33
95 % 179 272 47 Flexibility: Low
Max RMSD: 2.4, Avg RMSD: 0.7
PDBFlex
90 % 179 272 51
70 % 179 272 63
50 % 210 429 31
40 % 210 429 45
30 % 237 539 36
Entity #16 | Chains: N
30S RIBOSOMAL PROTEIN S14 protein, length: 60 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name Structural variation in cluster
100 % 179 270 37
95 % 179 270 55 Flexibility: Low
Max RMSD: 2.1, Avg RMSD: 0.9
PDBFlex
90 % 179 270 59
70 % 179 283 54
50 % 179 283 92
40 % 179 283 115
30 % 179 283 125
Entity #17 | Chains: O
30S RIBOSOMAL PROTEIN S15 protein, length: 88 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name Structural variation in cluster
100 % 179 274 30
95 % 183 279 38 Flexibility: Low
Max RMSD: 1.3, Avg RMSD: 0.5
PDBFlex
90 % 183 279 43
70 % 183 279 55
50 % 214 438 25
40 % 214 443 36
30 % 214 443 55
Entity #18 | 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 % 179 266 41
95 % 179 271 52 Flexibility: No
Max RMSD: 1.3, Avg RMSD: 0.4
PDBFlex
90 % 179 271 56
70 % 179 271 67
50 % 179 281 93
40 % 179 281 116
30 % 210 422 63
Entity #19 | Chains: Q
30S RIBOSOMAL PROTEIN S17 protein, length: 104 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name Structural variation in cluster
100 % 44 87 264
95 % 178 265 56 Flexibility: Low
Max RMSD: 1.9, Avg RMSD: 0.6
PDBFlex
90 % 179 269 60
70 % 179 269 70
50 % 179 269 96
40 % 179 269 119
30 % 179 269 128
Entity #2 | Chains: Y
ANTICODON STEM-LOOP OF SER TRANSFER RNA rna, length: 17 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
Entity #20 | Chains: R
30S RIBOSOMAL PROTEIN S18 protein, length: 88 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 23 51 733
95 % 162 236 65
90 % 162 236 70
70 % 162 236 84
50 % 162 236 118
40 % 162 236 140
30 % 162 236 147
Entity #21 | Chains: S
30S RIBOSOMAL PROTEIN S19 protein, length: 92 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name Structural variation in cluster
100 % 180 274 29
95 % 180 274 43 Flexibility: Low
Max RMSD: 3.7, Avg RMSD: 0.9
PDBFlex
90 % 180 274 48
70 % 180 274 59
50 % 208 431 28
40 % 208 434 41
30 % 208 434 58
Entity #22 | 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 % 160 219 53
95 % 179 270 53 Flexibility: Low
Max RMSD: 1.4, Avg RMSD: 0.7
PDBFlex
90 % 179 270 57
70 % 179 270 68
50 % 179 270 95
40 % 179 270 118
30 % 179 270 127
Entity #23 | Chains: V
30S RIBOSOMAL PROTEIN THX protein, length: 26 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name Structural variation in cluster
100 % 179 261 43
95 % 179 261 59 Flexibility: Low
Max RMSD: 1.2, Avg RMSD: 0.5
PDBFlex
90 % 179 261 63
70 % 179 261 75
50 % 179 261 102
40 % 179 261 124
30 % 179 261 135
Entity #3 | Chains: Z
A-SITE MESSENGER RNA FRAGMENT rna, length: 6 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
Entity #4 | 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 % 179 271 31
95 % 179 272 44 Flexibility: Low
Max RMSD: 9.2, Avg RMSD: 1.5
PDBFlex
90 % 179 272 49
70 % 179 272 60
50 % 207 418 34
40 % 207 423 46
30 % 207 423 62
Entity #5 | 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 % 162 235 49
95 % 162 235 66 Flexibility: Low
Max RMSD: 1.5, Avg RMSD: 0.7
PDBFlex
90 % 162 235 71
70 % 162 235 85
50 % 168 309 86
40 % 168 309 106
30 % 168 309 119
Entity #6 | Chains: D
30S RIBOSOMAL PROTEIN S4 protein, length: 208 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name Structural variation in cluster
100 % 177 264 42
95 % 179 272 45 Flexibility: Low
Max RMSD: 1.6, Avg RMSD: 0.5
PDBFlex
90 % 179 272 50
70 % 179 272 61
50 % 207 426 29
40 % 207 431 43
30 % 207 431 59
Entity #7 | Chains: E
30S RIBOSOMAL PROTEIN S5 protein, length: 161 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 179 271 35
95 % 179 271 49
90 % 179 271 53
70 % 179 271 64
50 % 208 426 30
40 % 208 426 44
30 % 208 428 61
Entity #8 | 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 % 181 276 27
95 % 187 282 37 Flexibility: Low
Max RMSD: 2.8, Avg RMSD: 0.8
PDBFlex
90 % 187 282 42
70 % 187 282 53
50 % 187 282 91
40 % 187 282 114
30 % 211 365 92
Entity #9 | Chains: G
30S RIBOSOMAL PROTEIN S7 protein, length: 155 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name Structural variation in cluster
100 % 180 275 28
95 % 180 276 42 Flexibility: Low
Max RMSD: 2.2, Avg RMSD: 0.8
PDBFlex
90 % 180 276 46
70 % 180 276 57
50 % 207 366 66
40 % 207 371 83
30 % 207 371 94

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.