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 % 26 297 39
95 % 26 297 49 Flexibility: Low
Max RMSD: 2.1, Avg RMSD: 1.1
PDBFlex
90 % 26 297 54
70 % 26 297 65
50 % 38 468 25
40 % 40 592 21
30 % 40 594 35
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 % 26 298 37
95 % 26 298 46 Flexibility: Low
Max RMSD: 1.9, Avg RMSD: 0.7
PDBFlex
90 % 26 298 51
70 % 26 298 63
50 % 32 462 33
40 % 36 601 20
30 % 36 601 34
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 % 23 266 49
95 % 26 305 37 Flexibility: Low
Max RMSD: 1.2, Avg RMSD: 0.7
PDBFlex
90 % 26 305 41
70 % 32 476 15
50 % 32 479 24
40 % 32 479 38
30 % 32 479 56
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 % 26 299 33
95 % 26 299 42 Flexibility: Low
Max RMSD: 2.4, Avg RMSD: 0.7
PDBFlex
90 % 26 299 48
70 % 26 299 60
50 % 32 466 31
40 % 32 466 44
30 % 34 598 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 % 26 297 38
95 % 26 297 48 Flexibility: Low
Max RMSD: 2.1, Avg RMSD: 0.8
PDBFlex
90 % 26 297 53
70 % 26 301 57
50 % 26 310 91
40 % 26 310 112
30 % 26 310 125
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 % 26 303 27
95 % 26 306 36 Flexibility: Low
Max RMSD: 1.3, Avg RMSD: 0.5
PDBFlex
90 % 26 306 40
70 % 26 306 51
50 % 35 474 26
40 % 35 479 37
30 % 35 479 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 % 26 293 40
95 % 26 298 44 Flexibility: No
Max RMSD: 1.3, Avg RMSD: 0.5
PDBFlex
90 % 26 298 49
70 % 26 298 61
50 % 26 308 93
40 % 32 464 46
30 % 32 464 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 % 26 269 46
95 % 26 295 51 Flexibility: Low
Max RMSD: 1.9, Avg RMSD: 0.6
PDBFlex
90 % 26 295 56
70 % 26 295 67
50 % 26 295 96
40 % 26 295 118
30 % 26 295 131
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 % 24 246 52
95 % 24 252 66 Flexibility: Low
Max RMSD: 8.4, Avg RMSD: 0.9
PDBFlex
90 % 24 252 70
70 % 24 252 84
50 % 24 252 115
40 % 24 252 137
30 % 24 252 147
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 % 27 301 30
95 % 27 301 39 Flexibility: Low
Max RMSD: 3.7, Avg RMSD: 0.9
PDBFlex
90 % 27 301 44
70 % 27 301 56
50 % 33 468 28
40 % 33 471 39
30 % 33 471 57
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 % 26 298 32
95 % 26 299 41 Flexibility: Low
Max RMSD: 9.2, Avg RMSD: 1.6
PDBFlex
90 % 26 299 46
70 % 26 299 59
50 % 32 452 35
40 % 32 458 47
30 % 32 458 64
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 % 26 258 50
95 % 26 297 50 Flexibility: Low
Max RMSD: 1.4, Avg RMSD: 0.7
PDBFlex
90 % 26 297 55
70 % 26 297 66
50 % 26 297 95
40 % 26 297 116
30 % 26 297 130
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 % 26 288 44
95 % 26 288 54 Flexibility: Low
Max RMSD: 1.2, Avg RMSD: 0.5
PDBFlex
90 % 26 288 60
70 % 26 288 72
50 % 26 288 100
40 % 26 288 122
30 % 26 288 132
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(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 % 24 251 51
95 % 24 251 67 Flexibility: Low
Max RMSD: 1.5, Avg RMSD: 0.7
PDBFlex
90 % 24 251 71
70 % 24 251 85
50 % 25 327 85
40 % 25 327 103
30 % 25 327 116
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 % 26 299 31
95 % 26 299 40 Flexibility: Low
Max RMSD: 1.6, Avg RMSD: 0.5
PDBFlex
90 % 26 299 45
70 % 26 299 58
50 % 32 462 30
40 % 32 468 41
30 % 32 468 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 % 26 298 36
95 % 26 298 45 Flexibility: Low
Max RMSD: 4.8, Avg RMSD: 0.6
PDBFlex
90 % 26 298 50
70 % 26 298 62
50 % 32 463 32
40 % 32 463 45
30 % 32 465 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 % 27 303 28
95 % 33 309 35 Flexibility: Low
Max RMSD: 2.9, Avg RMSD: 0.9
PDBFlex
90 % 33 309 39
70 % 33 309 50
50 % 33 309 90
40 % 33 309 111
30 % 40 398 90
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 % 27 303 29
95 % 27 303 38 Flexibility: Low
Max RMSD: 4.2, Avg RMSD: 0.8
PDBFlex
90 % 27 303 42
70 % 27 303 54
50 % 33 401 55
40 % 33 407 71
30 % 33 407 87
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 % 27 298 35
95 % 27 298 43 Flexibility: No
Max RMSD: 1.3, Avg RMSD: 0.4
PDBFlex
90 % 27 302 43
70 % 27 302 55
50 % 34 467 27
40 % 38 614 19
30 % 38 614 33
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 % 26 202 83
95 % 26 298 47 Flexibility: Low
Max RMSD: 1.5, Avg RMSD: 0.7
PDBFlex
90 % 26 298 52
70 % 26 298 64
50 % 32 456 34
40 % 32 457 48
30 % 34 596 37

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