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 % 214 333 28
95 % 214 333 49 Flexibility: No
Max RMSD: 1.3, Avg RMSD: 0.4
PDBFlex
90 % 215 337 49
70 % 215 337 57
50 % 246 543 22
40 % 246 549 28
30 % 280 739 23
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 % 52 101 238
95 % 214 333 51 Flexibility: Low
Max RMSD: 1.5, Avg RMSD: 0.7
PDBFlex
90 % 214 333 55
70 % 214 333 64
50 % 243 527 30
40 % 243 527 38
30 % 243 527 42
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 % 213 331 34
95 % 214 332 54 Flexibility: Low
Max RMSD: 2.2, Avg RMSD: 1.1
PDBFlex
90 % 214 332 58
70 % 214 332 67
50 % 244 538 24
40 % 244 538 32
30 % 244 571 31
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 % 214 333 31
95 % 214 333 52 Flexibility: Low
Max RMSD: 1.9, Avg RMSD: 0.7
PDBFlex
90 % 214 333 56
70 % 214 333 65
50 % 243 533 28
40 % 243 533 37
30 % 243 533 41
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 % 133 244 55
95 % 214 340 44 Flexibility: Low
Max RMSD: 1.2, Avg RMSD: 0.7
PDBFlex
90 % 214 340 48
70 % 244 537 15
50 % 244 554 20
40 % 244 554 27
30 % 244 554 33
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 % 214 334 29
95 % 214 334 48 Flexibility: Low
Max RMSD: 2.4, Avg RMSD: 0.7
PDBFlex
90 % 214 334 53
70 % 214 334 62
50 % 246 538 26
40 % 246 541 33
30 % 246 541 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 % 214 332 33
95 % 214 332 55 Flexibility: Low
Max RMSD: 2.1, Avg RMSD: 0.8
PDBFlex
90 % 214 332 59
70 % 214 339 56
50 % 214 352 87
40 % 214 352 103
30 % 214 352 105
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 % 214 336 27
95 % 218 341 43 Flexibility: Low
Max RMSD: 1.3, Avg RMSD: 0.5
PDBFlex
90 % 218 341 46
70 % 218 341 55
50 % 250 550 21
40 % 250 550 29
30 % 250 550 34
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 % 214 328 35
95 % 214 333 53 Flexibility: No
Max RMSD: 1.3, Avg RMSD: 0.5
PDBFlex
90 % 214 333 57
70 % 214 333 66
50 % 214 333 92
40 % 214 333 107
30 % 214 333 109
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 % 50 101 308
95 % 212 326 57 Flexibility: Low
Max RMSD: 2.0, Avg RMSD: 0.6
PDBFlex
90 % 213 330 61
70 % 213 330 69
50 % 213 330 94
40 % 213 330 110
30 % 213 330 112
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 % 26 54 857
95 % 187 277 71 Flexibility: Low
Max RMSD: 8.5, Avg RMSD: 0.9
PDBFlex
90 % 187 277 76
70 % 187 277 84
50 % 187 277 109
40 % 187 277 128
30 % 187 277 138
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 % 194 291 45
95 % 194 291 64 Flexibility: Low
Max RMSD: 3.7, Avg RMSD: 0.9
PDBFlex
90 % 194 291 71
70 % 215 336 58
50 % 244 540 23
40 % 244 540 31
30 % 244 540 36
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 % 194 276 48
95 % 214 332 56 Flexibility: Low
Max RMSD: 1.4, Avg RMSD: 0.7
PDBFlex
90 % 214 332 60
70 % 214 332 68
50 % 214 332 93
40 % 214 332 108
30 % 214 332 110
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 % 195 290 46
95 % 195 290 66 Flexibility: Low
Max RMSD: 1.2, Avg RMSD: 0.5
PDBFlex
90 % 195 290 73
70 % 195 290 82
50 % 195 290 104
40 % 195 290 124
30 % 195 290 131
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 % 214 332 30
95 % 214 334 47 Flexibility: Low
Max RMSD: 9.2, Avg RMSD: 1.5
PDBFlex
90 % 214 334 52
70 % 214 334 61
50 % 243 530 29
40 % 243 536 34
30 % 243 536 38
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 % 187 277 49
95 % 187 277 72 Flexibility: Low
Max RMSD: 1.5, Avg RMSD: 0.7
PDBFlex
90 % 187 277 77
70 % 187 277 85
50 % 193 357 86
40 % 193 357 102
30 % 193 357 103
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 % 212 326 36
95 % 214 334 46 Flexibility: Low
Max RMSD: 1.6, Avg RMSD: 0.5
PDBFlex
90 % 214 334 51
70 % 214 334 60
50 % 243 515 31
40 % 243 544 30
30 % 243 544 35
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 % 214 333 32
95 % 214 333 50 Flexibility: Low
Max RMSD: 4.8, Avg RMSD: 0.6
PDBFlex
90 % 214 333 54
70 % 214 333 63
50 % 244 534 27
40 % 244 534 36
30 % 244 534 40
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 % 216 338 25
95 % 222 344 38 Flexibility: Low
Max RMSD: 2.9, Avg RMSD: 0.8
PDBFlex
90 % 222 344 43
70 % 222 344 52
50 % 222 344 89
40 % 222 344 104
30 % 223 371 97
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 % 215 337 26
95 % 215 338 45 Flexibility: Low
Max RMSD: 4.2, Avg RMSD: 0.8
PDBFlex
90 % 215 338 50
70 % 215 336 59
50 % 244 471 54
40 % 244 477 66
30 % 244 477 69

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