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 % 92 268 39
95 % 92 269 53 Flexibility: Low
Max RMSD: 2.1, Avg RMSD: 1.1
PDBFlex
90 % 92 269 58
70 % 92 269 68
50 % 119 418 26
40 % 119 418 38
30 % 132 522 31
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 % 92 270 35
95 % 92 270 49 Flexibility: Low
Max RMSD: 1.9, Avg RMSD: 0.7
PDBFlex
90 % 92 270 54
70 % 92 270 64
50 % 113 412 33
40 % 128 522 19
30 % 128 522 32
Entity #12 | Chains: L
30S ribosomal protein S12 protein, length: 135 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 28 52 474
95 % 92 277 40
90 % 92 277 45
70 % 113 419 20
50 % 113 429 24
40 % 113 429 36
30 % 113 429 55
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 % 92 271 33
95 % 92 271 47 Flexibility: Low
Max RMSD: 2.4, Avg RMSD: 0.7
PDBFlex
90 % 92 271 52
70 % 92 271 62
50 % 114 416 31
40 % 114 416 44
30 % 127 520 34
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 % 92 269 38
95 % 92 269 54 Flexibility: Low
Max RMSD: 2.1, Avg RMSD: 0.9
PDBFlex
90 % 92 269 59
70 % 92 277 56
50 % 92 277 91
40 % 92 277 115
30 % 92 277 123
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 % 92 273 30
95 % 96 278 38 Flexibility: Low
Max RMSD: 1.3, Avg RMSD: 0.5
PDBFlex
90 % 96 278 43
70 % 96 278 54
50 % 120 425 25
40 % 120 430 35
30 % 120 430 54
Entity #16 | Chains: P
30S ribosomal protein S16 protein, length: 88 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 92 265 41
95 % 92 270 51
90 % 92 270 56
70 % 92 270 66
50 % 92 277 90
40 % 92 277 114
30 % 114 411 63
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 87 251
95 % 92 264 56 Flexibility: Low
Max RMSD: 1.9, Avg RMSD: 0.6
PDBFlex
90 % 92 268 60
70 % 92 268 69
50 % 92 268 93
40 % 92 268 117
30 % 92 268 128
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 % 79 184 56
95 % 85 235 65 Flexibility: Low
Max RMSD: 8.4, Avg RMSD: 0.9
PDBFlex
90 % 85 235 70
70 % 85 235 83
50 % 85 235 111
40 % 85 235 135
30 % 85 235 143
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 % 93 273 29
95 % 93 273 42 Flexibility: Low
Max RMSD: 3.7, Avg RMSD: 0.9
PDBFlex
90 % 93 273 48
70 % 93 273 59
50 % 114 418 28
40 % 114 421 39
30 % 114 421 56
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 % 92 270 31
95 % 92 271 44 Flexibility: Low
Max RMSD: 9.2, Avg RMSD: 1.7
PDBFlex
90 % 92 271 50
70 % 92 271 60
50 % 113 407 35
40 % 113 412 43
30 % 113 412 62
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 % 86 218 50
95 % 92 269 52 Flexibility: Low
Max RMSD: 1.4, Avg RMSD: 0.7
PDBFlex
90 % 92 269 57
70 % 92 269 67
50 % 92 269 92
40 % 92 269 116
30 % 92 269 127
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 % 92 260 43
95 % 92 260 59 Flexibility: Low
Max RMSD: 1.2, Avg RMSD: 0.5
PDBFlex
90 % 92 260 63
70 % 92 260 75
50 % 92 260 98
40 % 92 260 121
30 % 92 260 132
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 % 84 234 48
95 % 84 234 66 Flexibility: Low
Max RMSD: 1.5, Avg RMSD: 0.7
PDBFlex
90 % 84 234 71
70 % 84 234 84
50 % 88 308 84
40 % 88 308 103
30 % 88 308 115
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 % 92 263 42
95 % 92 271 45 Flexibility: Low
Max RMSD: 1.6, Avg RMSD: 0.5
PDBFlex
90 % 92 271 51
70 % 92 271 61
50 % 113 413 30
40 % 113 418 40
30 % 113 418 57
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 % 92 270 34
95 % 92 270 48 Flexibility: Low
Max RMSD: 4.8, Avg RMSD: 0.6
PDBFlex
90 % 92 270 53
70 % 92 270 63
50 % 114 415 29
40 % 114 415 42
30 % 114 417 60
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 % 94 275 27
95 % 100 281 37 Flexibility: Low
Max RMSD: 2.9, Avg RMSD: 0.9
PDBFlex
90 % 100 281 41
70 % 100 281 52
50 % 100 281 88
40 % 100 281 109
30 % 119 352 93
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 % 93 274 28
95 % 93 275 41 Flexibility: Low
Max RMSD: 4.2, Avg RMSD: 0.8
PDBFlex
90 % 93 275 46
70 % 93 275 57
50 % 112 353 68
40 % 112 358 85
30 % 112 358 95
Entity #8 | Chains: H
30S ribosomal protein S8 protein, length: 138 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 93 270 32
95 % 93 270 46
90 % 93 274 47
70 % 93 274 58
50 % 116 418 27
40 % 117 424 37
30 % 131 535 30
Entity #9 | Chains: I
30S ribosomal protein S9 protein, length: 128 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 82 179 68
95 % 92 270 50
90 % 92 270 55
70 % 92 270 65
50 % 113 409 34
40 % 113 409 47
30 % 126 517 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.