4DR7

Crystal structure of the Thermus thermophilus (HB8) 30S ribosomal subunit with codon, crystallographically disordered near-cognate transfer RNA anticodon stem-loop mismatched at the second codon position, and streptomycin bound


Sequence Similarity Clusters for the Entities in PDB 4DR7

Entity #1 | Chains: A
16S rRNA rna, length: 1522 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
Entity #10 | Chains: J
30S ribosomal protein S10 protein, length: 105 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name Structural variation in cluster
100 % 98 282 38
95 % 98 283 51 Flexibility: Low
Max RMSD: 2.0, Avg RMSD: 1.1
PDBFlex
90 % 98 283 56
70 % 98 283 67
50 % 125 446 27
40 % 125 446 40
30 % 139 560 34
Entity #11 | 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 % 98 284 35
95 % 98 284 47 Flexibility: Low
Max RMSD: 1.9, Avg RMSD: 0.7
PDBFlex
90 % 98 284 52
70 % 98 284 62
50 % 119 440 34
40 % 135 572 19
30 % 135 572 33
Entity #12 | 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 % 33 63 396
95 % 98 291 37 Flexibility: Low
Max RMSD: 1.2, Avg RMSD: 0.7
PDBFlex
90 % 98 291 43
70 % 119 444 18
50 % 119 457 24
40 % 119 457 37
30 % 119 457 57
Entity #13 | 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 % 98 285 32
95 % 98 285 44 Flexibility: Low
Max RMSD: 2.4, Avg RMSD: 0.7
PDBFlex
90 % 98 285 49
70 % 98 285 59
50 % 120 444 33
40 % 120 444 45
30 % 134 561 36
Entity #14 | Chains: N
30S ribosomal protein S14 protein, length: 61 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name Structural variation in cluster
100 % 98 283 36
95 % 98 283 52 Flexibility: Low
Max RMSD: 2.1, Avg RMSD: 0.9
PDBFlex
90 % 98 283 57
70 % 98 296 50
50 % 98 296 90
40 % 98 296 112
30 % 98 296 124
Entity #15 | Chains: O
30S ribosomal protein S15 protein, length: 89 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name Structural variation in cluster
100 % 98 287 29
95 % 102 292 36 Flexibility: Low
Max RMSD: 1.3, Avg RMSD: 0.5
PDBFlex
90 % 102 292 41
70 % 102 292 51
50 % 126 453 26
40 % 126 458 36
30 % 126 458 55
Entity #16 | 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 % 98 279 39
95 % 98 284 49 Flexibility: No
Max RMSD: 1.3, Avg RMSD: 0.4
PDBFlex
90 % 98 284 54
70 % 98 284 64
50 % 98 294 91
40 % 98 294 114
30 % 120 437 64
Entity #17 | Chains: Q
30S ribosomal protein S17 protein, length: 105 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name Structural variation in cluster
100 % 16 91 263
95 % 98 278 53 Flexibility: Low
Max RMSD: 1.9, Avg RMSD: 0.6
PDBFlex
90 % 98 282 58
70 % 98 282 68
50 % 98 282 96
40 % 98 282 119
30 % 98 282 128
Entity #18 | 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 % 83 190 61
95 % 89 241 66 Flexibility: Low
Max RMSD: 3.4, Avg RMSD: 0.8
PDBFlex
90 % 89 241 69
70 % 89 241 84
50 % 89 241 114
40 % 89 241 139
30 % 89 241 146
Entity #19 | Chains: S
30S ribosomal protein S19 protein, length: 93 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name Structural variation in cluster
100 % 99 287 28
95 % 99 287 39 Flexibility: Low
Max RMSD: 3.7, Avg RMSD: 0.9
PDBFlex
90 % 99 287 46
70 % 99 287 55
50 % 120 446 29
40 % 120 449 41
30 % 120 449 59
Entity #2 | 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 % 98 284 30
95 % 98 285 41 Flexibility: Low
Max RMSD: 9.2, Avg RMSD: 1.5
PDBFlex
90 % 98 285 47
70 % 98 285 56
50 % 119 433 36
40 % 119 438 46
30 % 119 438 62
Entity #20 | Chains: T
30S ribosomal protein S20 protein, length: 106 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 92 231 50
95 % 98 283 50
90 % 98 283 55
70 % 98 283 66
50 % 98 283 95
40 % 98 283 118
30 % 98 283 127
Entity #21 | Chains: U
30S ribosomal protein THX protein, length: 27 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 97 272 43
95 % 97 272 58
90 % 97 272 63
70 % 97 272 73
50 % 97 272 99
40 % 97 272 124
30 % 97 272 131
Entity #22 | Chains: V
5'-R(*UP*UP*UP*U)-3' rna, length: 4 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
Entity #23 | Chains: W
5'-R(*GP*CP*CP*UP*GP*GP*AP*AP*AP*GP*(PSU))-3' rna, length: 11 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
Entity #24 | Chains: a
5'-R(P*UP*GP*GP*AP*AP*AP*GP*(PSU))-3' rna, length: 8 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
Entity #25 | Chains: b
5'-R(P*UP*UP*U)-3' rna, length: 3 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
Entity #3 | 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 % 88 240 46
95 % 88 240 67 Flexibility: Low
Max RMSD: 1.5, Avg RMSD: 0.7
PDBFlex
90 % 88 240 70
70 % 88 240 85
50 % 92 315 86
40 % 92 315 104
30 % 92 315 118
Entity #4 | Chains: D
30S ribosomal protein S4 protein, length: 209 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name Structural variation in cluster
100 % 98 277 40
95 % 98 285 42 Flexibility: Low
Max RMSD: 1.6, Avg RMSD: 0.5
PDBFlex
90 % 98 285 48
70 % 98 285 57
50 % 119 441 30
40 % 119 446 42
30 % 119 446 60
Entity #5 | Chains: E
30S ribosomal protein S5 protein, length: 162 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name Structural variation in cluster
100 % 98 284 34
95 % 98 284 46 Flexibility: Low
Max RMSD: 4.8, Avg RMSD: 0.6
PDBFlex
90 % 98 284 51
70 % 98 284 61
50 % 120 441 32
40 % 120 441 44
30 % 120 443 61
Entity #6 | 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 % 100 289 26
95 % 106 295 35 Flexibility: Low
Max RMSD: 2.8, Avg RMSD: 0.8
PDBFlex
90 % 106 295 39
70 % 106 295 48
50 % 106 295 88
40 % 106 295 110
30 % 125 378 86
Entity #7 | Chains: G
30S ribosomal protein S7 protein, length: 156 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name Structural variation in cluster
100 % 99 288 27
95 % 99 289 38 Flexibility: Low
Max RMSD: 2.2, Avg RMSD: 0.8
PDBFlex
90 % 99 289 44
70 % 99 289 53
50 % 118 380 64
40 % 118 385 75
30 % 118 385 90
Entity #8 | 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 % 99 284 31
95 % 99 284 43 Flexibility: No
Max RMSD: 1.3, Avg RMSD: 0.4
PDBFlex
90 % 99 288 45
70 % 99 288 54
50 % 122 446 28
40 % 123 452 39
30 % 138 577 32
Entity #9 | Chains: I
30S ribosomal protein S9 protein, length: 128 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 88 191 64
95 % 98 284 48
90 % 98 284 53
70 % 98 284 63
50 % 119 435 35
40 % 119 435 47
30 % 133 561 35

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