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 % 194 292 29
95 % 194 292 42 Flexibility: No
Max RMSD: 1.3, Avg RMSD: 0.4
PDBFlex
90 % 195 296 43
70 % 195 296 52
50 % 225 457 27
40 % 226 464 39
30 % 259 592 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 % 49 94 226
95 % 194 292 46 Flexibility: Low
Max RMSD: 1.5, Avg RMSD: 0.8
PDBFlex
90 % 194 292 51
70 % 194 292 61
50 % 222 446 34
40 % 222 447 48
30 % 253 576 36
Entity #12 | Chains: J
30S RIBOSOMAL PROTEIN S10 protein, length: 104 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 193 290 34
95 % 194 291 49
90 % 194 291 54
70 % 194 291 65
50 % 228 458 25
40 % 228 458 40
30 % 259 575 34
Entity #13 | Chains: K
30S RIBOSOMAL PROTEIN S11 protein, length: 129 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 194 292 32
95 % 194 292 45
90 % 194 292 50
70 % 194 292 60
50 % 222 452 32
40 % 255 587 19
30 % 255 587 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 % 194 299 37 Flexibility: Low
Max RMSD: 1.2, Avg RMSD: 0.7
PDBFlex
90 % 194 299 41
70 % 222 456 17
50 % 222 469 24
40 % 222 470 37
30 % 222 470 56
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 % 194 293 30
95 % 194 293 43 Flexibility: Low
Max RMSD: 2.4, Avg RMSD: 0.7
PDBFlex
90 % 194 293 47
70 % 194 293 58
50 % 225 456 31
40 % 225 456 45
30 % 256 576 37
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 % 194 291 33
95 % 194 291 50 Flexibility: Low
Max RMSD: 2.1, Avg RMSD: 0.9
PDBFlex
90 % 194 291 55
70 % 194 304 49
50 % 194 304 89
40 % 194 304 111
30 % 194 304 122
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 % 194 295 27
95 % 198 300 36 Flexibility: Low
Max RMSD: 1.3, Avg RMSD: 0.5
PDBFlex
90 % 198 300 40
70 % 198 300 50
50 % 229 464 26
40 % 229 469 38
30 % 229 469 57
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 % 194 287 35
95 % 194 292 47 Flexibility: No
Max RMSD: 1.3, Avg RMSD: 0.4
PDBFlex
90 % 194 292 52
70 % 194 292 62
50 % 194 302 90
40 % 194 308 107
30 % 225 454 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 % 45 91 278
95 % 192 285 51 Flexibility: Low
Max RMSD: 1.9, Avg RMSD: 0.6
PDBFlex
90 % 193 289 56
70 % 193 289 66
50 % 193 289 94
40 % 193 289 117
30 % 193 289 127
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 51 755
95 % 171 246 65
90 % 171 246 69
70 % 171 246 85
50 % 171 246 114
40 % 171 246 139
30 % 171 246 144
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 % 195 295 26
95 % 195 295 39 Flexibility: Low
Max RMSD: 3.7, Avg RMSD: 0.9
PDBFlex
90 % 195 295 44
70 % 195 295 54
50 % 223 458 28
40 % 223 461 42
30 % 223 461 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 % 174 238 47
95 % 194 291 48 Flexibility: Low
Max RMSD: 1.4, Avg RMSD: 0.7
PDBFlex
90 % 194 291 53
70 % 194 291 64
50 % 194 291 93
40 % 194 291 116
30 % 194 291 126
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 % 194 282 41
95 % 194 282 55 Flexibility: Low
Max RMSD: 1.2, Avg RMSD: 0.5
PDBFlex
90 % 194 282 61
70 % 194 282 71
50 % 194 282 98
40 % 194 282 121
30 % 194 282 129
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 % 194 292 28
95 % 194 293 40 Flexibility: Low
Max RMSD: 9.2, Avg RMSD: 1.5
PDBFlex
90 % 194 293 45
70 % 194 293 55
50 % 222 444 35
40 % 222 450 46
30 % 222 450 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 % 171 245 46
95 % 171 245 66 Flexibility: Low
Max RMSD: 1.5, Avg RMSD: 0.7
PDBFlex
90 % 171 245 70
70 % 171 245 86
50 % 177 320 86
40 % 177 320 104
30 % 177 320 116
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 % 192 285 38
95 % 194 293 41 Flexibility: Low
Max RMSD: 1.6, Avg RMSD: 0.5
PDBFlex
90 % 194 293 46
70 % 194 293 57
50 % 222 452 29
40 % 222 458 43
30 % 222 458 59
Entity #7 | Chains: E
30S RIBOSOMAL PROTEIN S5 protein, length: 161 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 194 292 31
95 % 194 292 44
90 % 194 292 49
70 % 194 292 59
50 % 223 453 30
40 % 223 453 44
30 % 223 455 60
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 % 196 297 24
95 % 202 303 35 Flexibility: Low
Max RMSD: 2.8, Avg RMSD: 0.8
PDBFlex
90 % 202 303 39
70 % 202 303 48
50 % 202 303 88
40 % 202 303 109
30 % 226 389 85
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 % 195 296 25
95 % 195 297 38 Flexibility: Low
Max RMSD: 2.2, Avg RMSD: 0.8
PDBFlex
90 % 195 297 42
70 % 195 297 51
50 % 222 391 60
40 % 222 397 68
30 % 222 397 84

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