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 % 188 284 31
95 % 188 284 43 Flexibility: No
Max RMSD: 1.3, Avg RMSD: 0.4
PDBFlex
90 % 189 288 45
70 % 189 288 54
50 % 219 446 28
40 % 220 452 39
30 % 252 577 32
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 % 48 93 224
95 % 188 284 48 Flexibility: Low
Max RMSD: 1.5, Avg RMSD: 0.8
PDBFlex
90 % 188 284 53
70 % 188 284 63
50 % 216 435 35
40 % 216 435 47
30 % 246 561 35
Entity #12 | Chains: J
30S RIBOSOMAL PROTEIN S10 protein, length: 104 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 187 282 38
95 % 188 283 51
90 % 188 283 56
70 % 188 283 67
50 % 222 446 27
40 % 222 446 40
30 % 252 560 34
Entity #13 | Chains: K
30S RIBOSOMAL PROTEIN S11 protein, length: 129 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 188 284 35
95 % 188 284 47
90 % 188 284 52
70 % 188 284 62
50 % 216 440 34
40 % 248 572 19
30 % 248 572 33
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 % 122 220 54
95 % 188 291 37 Flexibility: Low
Max RMSD: 1.2, Avg RMSD: 0.7
PDBFlex
90 % 188 291 43
70 % 216 444 18
50 % 216 457 24
40 % 216 457 37
30 % 216 457 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 % 188 285 32
95 % 188 285 44 Flexibility: Low
Max RMSD: 2.4, Avg RMSD: 0.7
PDBFlex
90 % 188 285 49
70 % 188 285 59
50 % 219 444 33
40 % 219 444 45
30 % 249 561 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 % 188 283 36
95 % 188 283 52 Flexibility: Low
Max RMSD: 2.1, Avg RMSD: 0.9
PDBFlex
90 % 188 283 57
70 % 188 296 50
50 % 188 296 90
40 % 188 296 112
30 % 188 296 124
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 % 188 287 29
95 % 192 292 36 Flexibility: Low
Max RMSD: 1.3, Avg RMSD: 0.5
PDBFlex
90 % 192 292 41
70 % 192 292 51
50 % 223 453 26
40 % 223 458 36
30 % 223 458 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 % 188 279 39
95 % 188 284 49 Flexibility: No
Max RMSD: 1.3, Avg RMSD: 0.4
PDBFlex
90 % 188 284 54
70 % 188 284 64
50 % 188 294 91
40 % 188 294 114
30 % 219 437 64
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 % 45 91 263
95 % 187 278 53 Flexibility: Low
Max RMSD: 1.9, Avg RMSD: 0.6
PDBFlex
90 % 188 282 58
70 % 188 282 68
50 % 188 282 96
40 % 188 282 119
30 % 188 282 128
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 51 749
95 % 166 241 66
90 % 166 241 69
70 % 166 241 84
50 % 166 241 114
40 % 166 241 139
30 % 166 241 146
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 % 189 287 28
95 % 189 287 39 Flexibility: Low
Max RMSD: 3.7, Avg RMSD: 0.9
PDBFlex
90 % 189 287 46
70 % 189 287 55
50 % 217 446 29
40 % 217 449 41
30 % 217 449 59
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 % 169 231 50
95 % 188 283 50 Flexibility: Low
Max RMSD: 1.4, Avg RMSD: 0.7
PDBFlex
90 % 188 283 55
70 % 188 283 66
50 % 188 283 95
40 % 188 283 118
30 % 188 283 127
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 % 186 272 43
95 % 186 272 58 Flexibility: Low
Max RMSD: 1.2, Avg RMSD: 0.5
PDBFlex
90 % 186 272 63
70 % 186 272 73
50 % 186 272 99
40 % 186 272 124
30 % 186 272 131
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 % 188 284 30
95 % 188 285 41 Flexibility: Low
Max RMSD: 9.2, Avg RMSD: 1.5
PDBFlex
90 % 188 285 47
70 % 188 285 56
50 % 216 433 36
40 % 216 438 46
30 % 216 438 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 % 166 240 46
95 % 166 240 67 Flexibility: Low
Max RMSD: 1.5, Avg RMSD: 0.7
PDBFlex
90 % 166 240 70
70 % 166 240 85
50 % 172 315 86
40 % 172 315 104
30 % 172 315 118
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 % 186 277 40
95 % 188 285 42 Flexibility: Low
Max RMSD: 1.6, Avg RMSD: 0.5
PDBFlex
90 % 188 285 48
70 % 188 285 57
50 % 216 441 30
40 % 216 446 42
30 % 216 446 60
Entity #7 | Chains: E
30S RIBOSOMAL PROTEIN S5 protein, length: 161 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 188 284 34
95 % 188 284 46
90 % 188 284 51
70 % 188 284 61
50 % 217 441 32
40 % 217 441 44
30 % 217 443 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 % 190 289 26
95 % 196 295 35 Flexibility: Low
Max RMSD: 2.8, Avg RMSD: 0.8
PDBFlex
90 % 196 295 39
70 % 196 295 48
50 % 196 295 88
40 % 196 295 110
30 % 220 378 86
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 % 189 288 27
95 % 189 289 38 Flexibility: Low
Max RMSD: 2.2, Avg RMSD: 0.8
PDBFlex
90 % 189 289 44
70 % 189 289 53
50 % 216 380 64
40 % 216 385 75
30 % 216 385 90

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