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 % 62 91 229
95 % 218 272 50 Flexibility: Low
Max RMSD: 1.5, Avg RMSD: 0.8
PDBFlex
90 % 218 272 54
70 % 218 272 66
50 % 252 421 34
40 % 252 421 47
30 % 289 546 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 % 217 270 38
95 % 218 271 53 Flexibility: Low
Max RMSD: 2.0, Avg RMSD: 1.1
PDBFlex
90 % 218 271 57
70 % 218 271 69
50 % 258 432 26
40 % 258 432 40
30 % 295 545 34
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 % 218 272 35
95 % 218 272 49 Flexibility: Low
Max RMSD: 1.9, Avg RMSD: 0.7
PDBFlex
90 % 218 272 53
70 % 218 272 65
50 % 252 426 33
40 % 291 557 19
30 % 291 557 33
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 % 158 218 54
95 % 218 279 39 Flexibility: Low
Max RMSD: 1.2, Avg RMSD: 0.7
PDBFlex
90 % 218 279 44
70 % 252 430 18
50 % 252 443 24
40 % 252 443 38
30 % 252 443 57
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 % 218 273 33
95 % 218 273 47 Flexibility: Low
Max RMSD: 2.4, Avg RMSD: 0.7
PDBFlex
90 % 218 273 51
70 % 218 273 62
50 % 255 430 32
40 % 255 430 45
30 % 292 546 37
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 % 218 271 36
95 % 218 271 55 Flexibility: Low
Max RMSD: 2.1, Avg RMSD: 0.9
PDBFlex
90 % 218 271 59
70 % 218 284 54
50 % 218 284 92
40 % 218 284 115
30 % 218 284 124
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 % 218 275 30
95 % 222 280 38 Flexibility: Low
Max RMSD: 1.3, Avg RMSD: 0.5
PDBFlex
90 % 222 280 43
70 % 222 280 55
50 % 259 439 25
40 % 259 444 37
30 % 259 444 56
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 % 218 267 41
95 % 218 272 51 Flexibility: No
Max RMSD: 1.3, Avg RMSD: 0.4
PDBFlex
90 % 218 272 55
70 % 218 272 67
50 % 218 282 93
40 % 218 282 116
30 % 255 423 65
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 % 58 87 267
95 % 216 266 56 Flexibility: Low
Max RMSD: 1.9, Avg RMSD: 0.6
PDBFlex
90 % 218 270 60
70 % 218 270 70
50 % 218 270 97
40 % 218 270 120
30 % 218 270 128
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 % 31 51 737
95 % 195 237 66 Flexibility: Low
Max RMSD: 3.4, Avg RMSD: 0.8
PDBFlex
90 % 195 237 70
70 % 195 237 84
50 % 195 237 117
40 % 195 237 140
30 % 195 237 145
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 % 219 275 29
95 % 219 275 43 Flexibility: Low
Max RMSD: 3.7, Avg RMSD: 0.9
PDBFlex
90 % 219 275 48
70 % 219 275 59
50 % 253 432 29
40 % 253 435 41
30 % 253 435 59
Entity #21 | Chains: T
30S RIBOSOMAL PROTEIN S20 protein, length: 106 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 189 220 53
95 % 218 271 52
90 % 218 271 56
70 % 218 271 68
50 % 218 271 96
40 % 218 271 119
30 % 218 271 127
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 % 217 262 43
95 % 217 262 59 Flexibility: Low
Max RMSD: 1.2, Avg RMSD: 0.5
PDBFlex
90 % 217 262 63
70 % 217 262 75
50 % 217 262 102
40 % 217 262 125
30 % 217 262 133
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 % 218 272 31
95 % 218 273 44 Flexibility: Low
Max RMSD: 9.2, Avg RMSD: 1.5
PDBFlex
90 % 218 273 49
70 % 218 273 60
50 % 252 419 35
40 % 252 424 46
30 % 252 424 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 % 195 236 49
95 % 195 236 67 Flexibility: Low
Max RMSD: 1.5, Avg RMSD: 0.7
PDBFlex
90 % 195 236 71
70 % 195 236 85
50 % 207 310 86
40 % 207 310 106
30 % 207 310 118
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 % 216 265 42
95 % 218 273 45 Flexibility: Low
Max RMSD: 1.6, Avg RMSD: 0.5
PDBFlex
90 % 218 273 50
70 % 218 273 61
50 % 252 427 30
40 % 252 432 43
30 % 252 432 60
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 % 218 272 34
95 % 218 272 48 Flexibility: Low
Max RMSD: 4.8, Avg RMSD: 0.6
PDBFlex
90 % 218 272 52
70 % 218 272 63
50 % 253 427 31
40 % 253 427 44
30 % 253 429 62
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 % 220 277 27
95 % 226 283 37 Flexibility: Low
Max RMSD: 2.8, Avg RMSD: 0.8
PDBFlex
90 % 226 283 42
70 % 226 283 52
50 % 226 283 91
40 % 226 283 114
30 % 250 366 94
Entity #8 | Chains: G
30S RIBOSOMAL PROTEIN S7 protein, length: 155 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 219 276 28
95 % 219 277 40
90 % 219 277 45
70 % 219 277 56
50 % 247 367 66
40 % 247 372 84
30 % 247 372 96
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 % 217 272 32
95 % 217 272 46 Flexibility: No
Max RMSD: 1.3, Avg RMSD: 0.4
PDBFlex
90 % 219 276 46
70 % 219 276 57
50 % 255 432 28
40 % 256 438 39
30 % 295 562 32

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