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 35
95 % 109 334 57 Flexibility: Low
Max RMSD: 2.2, Avg RMSD: 1.1
PDBFlex
90 % 109 334 61
70 % 109 334 74
50 % 132 541 29
40 % 132 541 38
30 % 132 578 33
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 55 Flexibility: Low
Max RMSD: 1.9, Avg RMSD: 0.7
PDBFlex
90 % 109 335 59
70 % 109 335 72
50 % 131 539 31
40 % 131 539 40
30 % 131 539 43
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 55 756
95 % 109 342 44 Flexibility: Low
Max RMSD: 1.2, Avg RMSD: 0.7
PDBFlex
90 % 109 342 49
70 % 132 543 17
50 % 132 561 23
40 % 132 561 29
30 % 132 561 35
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 29
95 % 109 336 50 Flexibility: Low
Max RMSD: 2.4, Avg RMSD: 0.7
PDBFlex
90 % 109 336 55
70 % 109 336 68
50 % 132 545 28
40 % 132 548 36
30 % 132 548 40
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 34
95 % 109 334 58 Flexibility: Low
Max RMSD: 2.1, Avg RMSD: 0.8
PDBFlex
90 % 109 334 62
70 % 109 341 60
50 % 109 355 90
40 % 109 355 105
30 % 109 355 105
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 28
95 % 113 343 42 Flexibility: Low
Max RMSD: 1.3, Avg RMSD: 0.5
PDBFlex
90 % 113 343 47
70 % 113 343 58
50 % 138 557 24
40 % 138 557 31
30 % 138 557 36
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 36
95 % 109 335 53 Flexibility: No
Max RMSD: 1.3, Avg RMSD: 0.5
PDBFlex
90 % 109 335 57
70 % 109 335 70
50 % 109 335 95
40 % 109 335 110
30 % 109 335 112
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 % 16 101 321
95 % 109 328 59 Flexibility: Low
Max RMSD: 2.0, Avg RMSD: 0.6
PDBFlex
90 % 109 332 64
70 % 109 332 75
50 % 109 332 97
40 % 109 332 112
30 % 109 332 114
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 61
95 % 98 279 72 Flexibility: Low
Max RMSD: 8.5, Avg RMSD: 0.9
PDBFlex
90 % 98 279 77
70 % 98 279 89
50 % 98 279 112
40 % 98 279 132
30 % 98 279 142
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 64 Flexibility: Low
Max RMSD: 3.7, Avg RMSD: 0.9
PDBFlex
90 % 102 293 71
70 % 110 338 63
50 % 132 546 26
40 % 132 546 34
30 % 132 546 38
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 31
95 % 109 336 48 Flexibility: Low
Max RMSD: 9.2, Avg RMSD: 1.5
PDBFlex
90 % 109 336 54
70 % 109 336 66
50 % 131 537 32
40 % 131 543 37
30 % 131 543 41
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 56 Flexibility: Low
Max RMSD: 1.4, Avg RMSD: 0.7
PDBFlex
90 % 109 334 60
70 % 109 334 73
50 % 109 334 96
40 % 109 334 111
30 % 109 334 113
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 66 Flexibility: Low
Max RMSD: 1.2, Avg RMSD: 0.5
PDBFlex
90 % 100 292 73
70 % 100 292 84
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 73 Flexibility: Low
Max RMSD: 1.5, Avg RMSD: 0.7
PDBFlex
90 % 97 279 78
70 % 97 279 90
50 % 101 362 88
40 % 101 362 103
30 % 101 362 102
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 37
95 % 109 336 49 Flexibility: Low
Max RMSD: 1.6, Avg RMSD: 0.5
PDBFlex
90 % 109 336 53
70 % 109 336 65
50 % 109 360 87
40 % 131 551 33
30 % 131 551 37
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 32
95 % 109 335 52 Flexibility: Low
Max RMSD: 4.8, Avg RMSD: 0.6
PDBFlex
90 % 109 335 56
70 % 109 335 69
50 % 132 541 30
40 % 132 541 39
30 % 132 541 42
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 39 Flexibility: Low
Max RMSD: 2.9, Avg RMSD: 0.8
PDBFlex
90 % 119 348 44
70 % 119 348 55
50 % 119 348 91
40 % 119 348 106
30 % 119 348 106
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 51
70 % 110 338 64
50 % 131 475 54
40 % 131 481 70
30 % 131 481 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 51 Flexibility: No
Max RMSD: 1.3, Avg RMSD: 0.4
PDBFlex
90 % 110 339 52
70 % 110 339 62
50 % 134 550 25
40 % 134 556 30
30 % 149 752 22
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 63
95 % 109 335 54 Flexibility: Low
Max RMSD: 1.5, Avg RMSD: 0.7
PDBFlex
90 % 109 335 58
70 % 109 335 71
50 % 131 534 33
40 % 131 534 41
30 % 131 534 44

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