1N34

Structure of the Thermus thermophilus 30S ribosomal subunit in the presence of codon and crystallographically disordered near-cognate transfer rna anticodon stem-loop mismatched at the first codon position


Sequence Similarity Clusters for the Entities in PDB 1N34

Entity #1 | Chains: A
16S RIBOSOMAL RNA rna, length: 1522 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
Entity #10 | 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 % 64 96 229
95 % 235 295 47 Flexibility: Low
Max RMSD: 1.5, Avg RMSD: 0.8
PDBFlex
90 % 235 295 51
70 % 235 295 63
50 % 269 452 34
40 % 269 453 48
30 % 307 582 35
Entity #11 | 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 % 235 294 40
95 % 235 294 49 Flexibility: Low
Max RMSD: 2.0, Avg RMSD: 1.1
PDBFlex
90 % 235 294 53
70 % 235 294 64
50 % 275 464 25
40 % 313 579 20
30 % 313 581 33
Entity #12 | 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 % 235 295 37
95 % 235 295 46 Flexibility: Low
Max RMSD: 1.9, Avg RMSD: 0.7
PDBFlex
90 % 235 295 50
70 % 235 295 62
50 % 269 458 32
40 % 309 585 19
30 % 309 585 32
Entity #13 | 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 % 207 263 49
95 % 235 302 37 Flexibility: Low
Max RMSD: 1.2, Avg RMSD: 0.7
PDBFlex
90 % 235 302 41
70 % 269 472 15
50 % 269 475 24
40 % 269 475 38
30 % 269 475 55
Entity #14 | 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 % 235 296 34
95 % 235 296 42 Flexibility: Low
Max RMSD: 2.4, Avg RMSD: 0.7
PDBFlex
90 % 235 296 47
70 % 235 296 59
50 % 272 462 30
40 % 272 462 43
30 % 310 582 36
Entity #15 | 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 % 235 294 39
95 % 235 294 48 Flexibility: Low
Max RMSD: 2.1, Avg RMSD: 0.9
PDBFlex
90 % 235 294 52
70 % 235 298 55
50 % 235 307 91
40 % 235 307 112
30 % 235 307 126
Entity #16 | 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 % 236 300 27
95 % 239 303 36 Flexibility: Low
Max RMSD: 1.3, Avg RMSD: 0.5
PDBFlex
90 % 239 303 40
70 % 239 303 51
50 % 276 470 26
40 % 276 475 37
30 % 276 475 54
Entity #17 | 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 % 235 290 41
95 % 235 295 44 Flexibility: No
Max RMSD: 1.3, Avg RMSD: 0.4
PDBFlex
90 % 235 295 48
70 % 235 295 60
50 % 235 305 92
40 % 272 460 45
30 % 272 460 61
Entity #18 | 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 % 17 26 1695
95 % 234 292 51 Flexibility: Low
Max RMSD: 1.9, Avg RMSD: 0.6
PDBFlex
90 % 234 292 55
70 % 234 292 67
50 % 234 292 95
40 % 234 292 117
30 % 234 292 132
Entity #19 | 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 % 201 243 54
95 % 204 249 64 Flexibility: Low
Max RMSD: 3.4, Avg RMSD: 0.8
PDBFlex
90 % 204 249 68
70 % 204 249 85
50 % 204 249 116
40 % 204 249 138
30 % 204 249 150
Entity #2 | Chains: Z
A-SITE MESSENGER RNA FRAGMENT rna, length: 6 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
Entity #20 | 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 % 236 298 30
95 % 236 298 39 Flexibility: Low
Max RMSD: 3.7, Avg RMSD: 0.9
PDBFlex
90 % 236 298 44
70 % 236 298 54
50 % 270 464 28
40 % 270 467 41
30 % 270 467 58
Entity #21 | Chains: T
30S RIBOSOMAL PROTEIN S20 protein, length: 106 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 209 255 50
95 % 235 294 50
90 % 235 294 54
70 % 235 294 65
50 % 235 294 94
40 % 235 294 116
30 % 235 294 131
Entity #22 | 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 % 234 285 44
95 % 234 285 54 Flexibility: Low
Max RMSD: 1.2, Avg RMSD: 0.5
PDBFlex
90 % 234 285 59
70 % 234 285 71
50 % 234 285 100
40 % 234 285 121
30 % 234 285 135
Entity #3 | 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 % 235 295 33
95 % 235 296 41 Flexibility: Low
Max RMSD: 9.2, Avg RMSD: 1.5
PDBFlex
90 % 235 296 46
70 % 235 296 58
50 % 269 448 36
40 % 269 454 47
30 % 269 454 63
Entity #4 | 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 % 204 248 51
95 % 204 248 65 Flexibility: Low
Max RMSD: 1.5, Avg RMSD: 0.7
PDBFlex
90 % 204 248 69
70 % 204 248 87
50 % 216 323 87
40 % 216 323 105
30 % 216 323 120
Entity #5 | 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 % 235 296 32
95 % 235 296 40 Flexibility: Low
Max RMSD: 1.6, Avg RMSD: 0.5
PDBFlex
90 % 235 296 45
70 % 235 296 57
50 % 269 458 29
40 % 269 464 42
30 % 269 464 59
Entity #6 | 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 % 235 295 36
95 % 235 295 45 Flexibility: Low
Max RMSD: 4.8, Avg RMSD: 0.6
PDBFlex
90 % 235 295 49
70 % 235 295 61
50 % 270 459 31
40 % 270 459 44
30 % 270 461 60
Entity #7 | 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 % 237 300 28
95 % 243 306 35 Flexibility: Low
Max RMSD: 2.8, Avg RMSD: 0.8
PDBFlex
90 % 243 306 39
70 % 243 306 50
50 % 243 306 90
40 % 243 306 111
30 % 267 395 86
Entity #8 | Chains: G
30S RIBOSOMAL PROTEIN S7 protein, length: 155 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 236 300 29
95 % 236 300 38
90 % 236 300 42
70 % 236 300 52
50 % 264 397 54
40 % 264 403 67
30 % 264 403 81
Entity #9 | 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 % 234 295 35
95 % 234 295 43 Flexibility: No
Max RMSD: 1.3, Avg RMSD: 0.4
PDBFlex
90 % 236 299 43
70 % 236 299 53
50 % 272 463 27
40 % 313 598 18
30 % 313 598 31

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