4DR6

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


Sequence Similarity Clusters for the Entities in PDB 4DR6

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 % 23 269 39
95 % 23 270 53 Flexibility: Low
Max RMSD: 2.1, Avg RMSD: 1.1
PDBFlex
90 % 23 270 58
70 % 23 270 69
50 % 35 428 26
40 % 35 428 38
30 % 37 535 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 % 23 271 35
95 % 23 271 49 Flexibility: Low
Max RMSD: 1.9, Avg RMSD: 0.7
PDBFlex
90 % 23 271 54
70 % 23 271 65
50 % 29 422 32
40 % 33 546 19
30 % 33 546 31
Entity #12 | Chains: L
30S ribosomal protein S12 protein, length: 135 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 10 53 476
95 % 23 278 39
90 % 23 278 44
70 % 29 426 18
50 % 29 439 24
40 % 29 439 36
30 % 29 439 56
Entity #13 | Chains: M
30S ribosomal protein S13 protein, length: 126 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 23 272 33
95 % 23 272 46
90 % 23 272 51
70 % 23 272 62
50 % 29 426 31
40 % 29 426 44
30 % 31 535 35
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 % 23 270 36
95 % 23 270 54 Flexibility: Low
Max RMSD: 2.1, Avg RMSD: 0.8
PDBFlex
90 % 23 270 59
70 % 23 283 53
50 % 23 283 91
40 % 23 283 112
30 % 23 283 124
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 % 23 274 30
95 % 23 279 38 Flexibility: Low
Max RMSD: 1.3, Avg RMSD: 0.5
PDBFlex
90 % 23 279 43
70 % 23 279 54
50 % 32 435 25
40 % 32 440 35
30 % 32 440 55
Entity #16 | Chains: P
30S ribosomal protein S16 protein, length: 88 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 23 266 41
95 % 23 271 51
90 % 23 271 56
70 % 23 271 67
50 % 23 281 92
40 % 23 281 114
30 % 29 419 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 % 1 87 259
95 % 23 265 56 Flexibility: Low
Max RMSD: 1.9, Avg RMSD: 0.6
PDBFlex
90 % 23 269 60
70 % 23 269 70
50 % 23 269 95
40 % 23 269 117
30 % 23 269 128
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 % 21 185 57
95 % 21 236 65 Flexibility: Low
Max RMSD: 8.4, Avg RMSD: 0.9
PDBFlex
90 % 21 236 69
70 % 21 236 81
50 % 21 236 114
40 % 21 236 137
30 % 21 236 145
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 % 24 274 29
95 % 24 274 42 Flexibility: Low
Max RMSD: 3.7, Avg RMSD: 0.9
PDBFlex
90 % 24 274 48
70 % 24 274 58
50 % 30 428 28
40 % 30 431 40
30 % 30 431 57
Entity #2 | Chains: B
30S ribosomal protein S2 protein, length: 256 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 23 271 31
95 % 23 272 43
90 % 23 272 49
70 % 23 272 59
50 % 29 415 34
40 % 29 420 45
30 % 29 420 61
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 % 23 219 51
95 % 23 270 52 Flexibility: Low
Max RMSD: 1.4, Avg RMSD: 0.7
PDBFlex
90 % 23 270 57
70 % 23 270 68
50 % 23 270 94
40 % 23 270 116
30 % 23 270 127
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 % 23 261 43
95 % 23 261 59 Flexibility: Low
Max RMSD: 1.1, Avg RMSD: 0.5
PDBFlex
90 % 23 261 63
70 % 23 261 74
50 % 23 261 100
40 % 23 261 122
30 % 23 261 135
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(P*UP*UP*GP*AP*GP*GP*(PSU)P*GP*G)-3' rna, length: 9 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
Entity #24 | Chains: a
5'-R(P*CP*UP*UP*GP*AP*GP*GP*(PSU)P*GP*GP*U)-3' rna, length: 11 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
Entity #25 | Chains: b
5'-R(*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 % 21 235 49
95 % 21 235 66 Flexibility: Low
Max RMSD: 1.5, Avg RMSD: 0.7
PDBFlex
90 % 21 235 70
70 % 21 235 82
50 % 22 309 85
40 % 22 309 103
30 % 22 309 118
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 % 23 264 42
95 % 23 272 44 Flexibility: Low
Max RMSD: 1.6, Avg RMSD: 0.5
PDBFlex
90 % 23 272 50
70 % 23 272 60
50 % 29 423 29
40 % 29 428 42
30 % 29 428 58
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 % 23 271 34
95 % 23 271 48 Flexibility: Low
Max RMSD: 4.7, Avg RMSD: 0.6
PDBFlex
90 % 23 271 53
70 % 23 271 64
50 % 29 423 30
40 % 29 423 43
30 % 29 425 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 % 24 276 27
95 % 30 282 37 Flexibility: Low
Max RMSD: 2.8, Avg RMSD: 0.8
PDBFlex
90 % 30 282 42
70 % 30 282 52
50 % 30 282 90
40 % 30 282 111
30 % 37 362 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 % 24 275 28
95 % 24 276 41 Flexibility: Low
Max RMSD: 4.2, Avg RMSD: 0.9
PDBFlex
90 % 24 276 46
70 % 24 276 56
50 % 30 363 66
40 % 30 368 82
30 % 30 368 95
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 % 24 271 32
95 % 24 271 45 Flexibility: No
Max RMSD: 1.3, Avg RMSD: 0.4
PDBFlex
90 % 24 275 47
70 % 24 275 57
50 % 31 428 27
40 % 32 434 37
30 % 35 551 30
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 % 23 180 69
95 % 23 271 50 Flexibility: Low
Max RMSD: 1.5, Avg RMSD: 0.8
PDBFlex
90 % 23 271 55
70 % 23 271 66
50 % 29 417 33
40 % 29 417 46
30 % 31 535 34

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.