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 % 109 333 36
95 % 109 334 58 Flexibility: Low
Max RMSD: 2.2, Avg RMSD: 1.1
PDBFlex
90 % 109 334 63
70 % 109 334 75
50 % 132 549 26
40 % 132 549 34
30 % 132 586 32
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 % 109 335 33
95 % 109 335 56 Flexibility: Low
Max RMSD: 1.9, Avg RMSD: 0.7
PDBFlex
90 % 109 335 61
70 % 109 335 72
50 % 131 543 29
40 % 131 543 38
30 % 131 543 41
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 % 23 55 781
95 % 109 342 45 Flexibility: Low
Max RMSD: 1.2, Avg RMSD: 0.7
PDBFlex
90 % 109 342 51
70 % 132 547 17
50 % 132 565 22
40 % 132 565 28
30 % 132 565 33
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 % 109 336 31
95 % 109 336 52 Flexibility: Low
Max RMSD: 2.4, Avg RMSD: 0.7
PDBFlex
90 % 109 336 57
70 % 109 336 69
50 % 132 549 27
40 % 132 552 35
30 % 132 552 38
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 % 109 334 35
95 % 109 334 59 Flexibility: Low
Max RMSD: 2.1, Avg RMSD: 0.8
PDBFlex
90 % 109 334 64
70 % 109 341 61
50 % 109 355 90
40 % 109 355 104
30 % 109 355 106
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 % 109 338 29
95 % 113 343 43 Flexibility: Low
Max RMSD: 1.3, Avg RMSD: 0.5
PDBFlex
90 % 113 343 48
70 % 113 343 58
50 % 138 561 23
40 % 138 561 30
30 % 138 561 34
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 % 109 330 37
95 % 109 335 53 Flexibility: No
Max RMSD: 1.3, Avg RMSD: 0.5
PDBFlex
90 % 109 335 58
70 % 109 335 70
50 % 109 335 95
40 % 109 335 111
30 % 109 335 116
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 % 16 101 331
95 % 109 328 60 Flexibility: Low
Max RMSD: 2.0, Avg RMSD: 0.6
PDBFlex
90 % 109 332 65
70 % 109 332 76
50 % 109 332 97
40 % 109 332 113
30 % 109 332 119
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 % 92 225 60
95 % 98 279 76 Flexibility: Low
Max RMSD: 8.5, Avg RMSD: 0.9
PDBFlex
90 % 98 279 80
70 % 98 279 91
50 % 98 279 111
40 % 98 279 129
30 % 98 279 140
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 % 102 293 44
95 % 102 293 67 Flexibility: Low
Max RMSD: 3.7, Avg RMSD: 0.9
PDBFlex
90 % 102 293 71
70 % 110 338 63
50 % 132 550 25
40 % 132 550 33
30 % 132 550 37
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 % 109 334 32
95 % 109 336 48 Flexibility: Low
Max RMSD: 9.2, Avg RMSD: 1.5
PDBFlex
90 % 109 336 55
70 % 109 336 66
50 % 131 541 30
40 % 131 547 36
30 % 131 547 39
Entity #20 | 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 % 103 278 48
95 % 109 334 57 Flexibility: Low
Max RMSD: 1.4, Avg RMSD: 0.7
PDBFlex
90 % 109 334 62
70 % 109 334 74
50 % 109 334 96
40 % 109 334 112
30 % 109 334 117
Entity #21 | Chains: U
30S ribosomal protein THX protein, length: 27 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name Structural variation in cluster
100 % 100 292 46
95 % 100 292 69 Flexibility: Low
Max RMSD: 1.2, Avg RMSD: 0.5
PDBFlex
90 % 100 292 74
70 % 100 292 85
50 % 100 292 107
40 % 100 292 127
30 % 100 292 137
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 % 97 279 49
95 % 97 279 75 Flexibility: Low
Max RMSD: 1.5, Avg RMSD: 0.7
PDBFlex
90 % 97 279 79
70 % 97 279 90
50 % 101 366 87
40 % 101 366 102
30 % 101 366 104
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 % 109 328 38
95 % 109 336 49 Flexibility: Low
Max RMSD: 1.6, Avg RMSD: 0.5
PDBFlex
90 % 109 336 56
70 % 109 336 67
50 % 109 360 89
40 % 131 555 31
30 % 131 555 35
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 % 109 335 34
95 % 109 335 55 Flexibility: Low
Max RMSD: 4.8, Avg RMSD: 0.6
PDBFlex
90 % 109 335 60
70 % 109 335 73
50 % 132 545 28
40 % 132 545 37
30 % 132 545 40
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 % 111 340 26
95 % 119 348 40 Flexibility: Low
Max RMSD: 2.9, Avg RMSD: 0.8
PDBFlex
90 % 119 348 44
70 % 119 348 56
50 % 119 348 91
40 % 119 348 106
30 % 119 348 109
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 % 110 339 27
95 % 110 340 47 Flexibility: Low
Max RMSD: 4.2, Avg RMSD: 0.8
PDBFlex
90 % 110 340 54
70 % 110 338 65
50 % 131 479 52
40 % 131 485 68
30 % 131 485 71
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 % 110 335 30
95 % 110 335 50 Flexibility: No
Max RMSD: 1.3, Avg RMSD: 0.4
PDBFlex
90 % 110 339 53
70 % 110 339 62
50 % 111 364 86
40 % 134 560 29
30 % 149 763 21
Entity #9 | 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 % 99 234 62
95 % 109 335 54 Flexibility: Low
Max RMSD: 1.5, Avg RMSD: 0.7
PDBFlex
90 % 109 335 59
70 % 109 335 71
50 % 131 538 31
40 % 131 538 39
30 % 131 538 43

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