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 % 195 295 35
95 % 195 295 43 Flexibility: No
Max RMSD: 1.3, Avg RMSD: 0.4
PDBFlex
90 % 196 299 43
70 % 196 299 54
50 % 226 463 27
40 % 260 607 18
30 % 260 607 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 96 231
95 % 195 295 47 Flexibility: Low
Max RMSD: 1.5, Avg RMSD: 0.7
PDBFlex
90 % 195 295 51
70 % 195 295 63
50 % 223 452 35
40 % 223 453 49
30 % 254 589 35
Entity #12 | Chains: J
30S RIBOSOMAL PROTEIN S10 protein, length: 104 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name Structural variation in cluster
100 % 195 294 40
95 % 195 294 49 Flexibility: Low
Max RMSD: 2.1, Avg RMSD: 1.1
PDBFlex
90 % 195 294 53
70 % 195 294 64
50 % 229 464 25
40 % 260 585 20
30 % 260 587 34
Entity #13 | 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 % 195 295 37
95 % 195 295 46 Flexibility: Low
Max RMSD: 1.9, Avg RMSD: 0.7
PDBFlex
90 % 195 295 50
70 % 195 295 62
50 % 223 458 32
40 % 256 594 19
30 % 256 594 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 % 171 263 49
95 % 195 302 37 Flexibility: Low
Max RMSD: 1.2, Avg RMSD: 0.7
PDBFlex
90 % 195 302 41
70 % 223 472 15
50 % 223 475 24
40 % 223 475 38
30 % 223 475 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 % 195 296 34
95 % 195 296 42 Flexibility: Low
Max RMSD: 2.4, Avg RMSD: 0.7
PDBFlex
90 % 195 296 47
70 % 195 296 59
50 % 226 462 30
40 % 226 462 43
30 % 257 591 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 % 195 294 39
95 % 195 294 48 Flexibility: Low
Max RMSD: 2.1, Avg RMSD: 0.8
PDBFlex
90 % 195 294 52
70 % 195 298 56
50 % 195 307 92
40 % 195 307 114
30 % 195 307 126
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 % 196 300 27
95 % 199 303 36 Flexibility: Low
Max RMSD: 1.3, Avg RMSD: 0.5
PDBFlex
90 % 199 303 40
70 % 199 303 52
50 % 230 470 26
40 % 230 475 37
30 % 230 475 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 % 195 290 42
95 % 195 295 44 Flexibility: No
Max RMSD: 1.3, Avg RMSD: 0.5
PDBFlex
90 % 195 295 48
70 % 195 295 60
50 % 195 305 93
40 % 226 460 46
30 % 226 460 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 % 12 26 1704
95 % 194 292 51 Flexibility: Low
Max RMSD: 1.9, Avg RMSD: 0.6
PDBFlex
90 % 194 292 55
70 % 194 292 68
50 % 194 292 96
40 % 194 292 118
30 % 194 292 131
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 Structural variation in cluster
100 % 171 243 54
95 % 172 249 64 Flexibility: Low
Max RMSD: 8.4, Avg RMSD: 0.9
PDBFlex
90 % 172 249 68
70 % 172 249 86
50 % 172 249 117
40 % 172 249 139
30 % 172 249 148
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 % 196 298 30
95 % 196 298 39 Flexibility: Low
Max RMSD: 3.7, Avg RMSD: 0.9
PDBFlex
90 % 196 298 44
70 % 196 298 55
50 % 224 464 28
40 % 224 467 41
30 % 224 467 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 % 177 255 50
95 % 195 294 50 Flexibility: Low
Max RMSD: 1.4, Avg RMSD: 0.7
PDBFlex
90 % 195 294 54
70 % 195 294 65
50 % 195 294 94
40 % 195 294 116
30 % 195 294 130
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 % 195 285 44
95 % 195 285 54 Flexibility: Low
Max RMSD: 1.2, Avg RMSD: 0.5
PDBFlex
90 % 195 285 59
70 % 195 285 71
50 % 195 285 100
40 % 195 285 123
30 % 195 285 134
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 % 195 295 33
95 % 195 296 41 Flexibility: Low
Max RMSD: 9.2, Avg RMSD: 1.6
PDBFlex
90 % 195 296 46
70 % 195 296 58
50 % 223 448 36
40 % 223 454 47
30 % 223 454 64
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 % 172 248 51
95 % 172 248 65 Flexibility: Low
Max RMSD: 1.5, Avg RMSD: 0.7
PDBFlex
90 % 172 248 70
70 % 172 248 88
50 % 178 323 87
40 % 178 323 105
30 % 178 323 119
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 % 195 296 32
95 % 195 296 40 Flexibility: Low
Max RMSD: 1.6, Avg RMSD: 0.5
PDBFlex
90 % 195 296 45
70 % 195 296 57
50 % 223 458 29
40 % 223 464 42
30 % 223 464 60
Entity #7 | Chains: E
30S RIBOSOMAL PROTEIN S5 protein, length: 161 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name Structural variation in cluster
100 % 195 295 36
95 % 195 295 45 Flexibility: Low
Max RMSD: 4.8, Avg RMSD: 0.6
PDBFlex
90 % 195 295 49
70 % 195 295 61
50 % 224 459 31
40 % 224 459 44
30 % 224 461 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 % 197 300 28
95 % 203 306 35 Flexibility: Low
Max RMSD: 2.9, Avg RMSD: 0.9
PDBFlex
90 % 203 306 39
70 % 203 306 50
50 % 203 306 91
40 % 203 306 113
30 % 227 395 88
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 % 196 300 29
95 % 196 300 38 Flexibility: Low
Max RMSD: 4.2, Avg RMSD: 0.8
PDBFlex
90 % 196 300 42
70 % 196 300 53
50 % 223 397 56
40 % 223 403 72
30 % 223 403 87

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