4GKK

Structure of the Thermus thermophilus 30S ribosomal subunit complexed with a human mitochondrial anticodon stem loop (ASL) of transfer RNA Methionine (TRNAMET) bound to an mRNA with an AUA-codon in the A-site and paromomycin


Sequence Similarity Clusters for the Entities in PDB 4GKK

Entity #1 | Chains: A
16S rRNA rna, length: 1513 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
Entity #10 | Chains: J
30S ribosomal protein S10 protein, length: 98 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name Structural variation in cluster
100 % 106 297 38
95 % 106 297 48 Flexibility: Low
Max RMSD: 2.1, Avg RMSD: 1.1
PDBFlex
90 % 106 297 53
70 % 106 297 64
50 % 133 468 24
40 % 147 592 20
30 % 147 594 34
Entity #11 | Chains: K
30S ribosomal protein S11 protein, length: 119 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name Structural variation in cluster
100 % 106 298 36
95 % 106 298 45 Flexibility: Low
Max RMSD: 1.9, Avg RMSD: 0.7
PDBFlex
90 % 106 298 50
70 % 106 298 62
50 % 127 462 32
40 % 143 601 19
30 % 143 601 33
Entity #12 | Chains: L
30S ribosomal protein S12 protein, length: 124 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name Structural variation in cluster
100 % 90 266 48
95 % 106 305 36 Flexibility: Low
Max RMSD: 1.2, Avg RMSD: 0.7
PDBFlex
90 % 106 305 40
70 % 127 476 14
50 % 127 479 23
40 % 127 479 37
30 % 127 479 56
Entity #13 | Chains: M
30S ribosomal protein S13 protein, length: 125 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name Structural variation in cluster
100 % 106 299 32
95 % 106 299 41 Flexibility: Low
Max RMSD: 2.4, Avg RMSD: 0.7
PDBFlex
90 % 106 299 47
70 % 106 299 59
50 % 128 466 30
40 % 128 466 43
30 % 142 598 37
Entity #14 | Chains: N
30S ribosomal protein S14 type Z protein, length: 60 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name Structural variation in cluster
100 % 106 297 37
95 % 106 297 47 Flexibility: Low
Max RMSD: 2.1, Avg RMSD: 0.8
PDBFlex
90 % 106 297 52
70 % 106 301 56
50 % 106 310 90
40 % 106 310 111
30 % 106 310 124
Entity #15 | Chains: O
30S ribosomal protein S15 protein, length: 88 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name Structural variation in cluster
100 % 107 303 26
95 % 110 306 35 Flexibility: Low
Max RMSD: 1.3, Avg RMSD: 0.5
PDBFlex
90 % 110 306 39
70 % 110 306 50
50 % 134 474 25
40 % 134 479 36
30 % 134 479 55
Entity #16 | Chains: P
30S ribosomal protein S16 protein, length: 83 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name Structural variation in cluster
100 % 106 293 39
95 % 106 298 43 Flexibility: No
Max RMSD: 1.3, Avg RMSD: 0.5
PDBFlex
90 % 106 298 48
70 % 106 298 60
50 % 106 308 92
40 % 128 464 45
30 % 128 464 63
Entity #17 | Chains: Q
30S ribosomal protein S17 protein, length: 104 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name Structural variation in cluster
100 % 6 26 1717
95 % 106 295 50 Flexibility: Low
Max RMSD: 1.9, Avg RMSD: 0.6
PDBFlex
90 % 106 295 55
70 % 106 295 66
50 % 106 295 95
40 % 106 295 117
30 % 106 295 130
Entity #18 | Chains: R
30S ribosomal protein S18 protein, length: 73 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name Structural variation in cluster
100 % 12 48 571
95 % 12 48 711 Flexibility: Low
Max RMSD: 1.3, Avg RMSD: 0.7
PDBFlex
90 % 12 48 737
70 % 12 48 785
50 % 12 48 845
40 % 12 48 869
30 % 12 48 867
Entity #19 | Chains: S
30S ribosomal protein S19 protein, length: 80 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name Structural variation in cluster
100 % 107 301 29
95 % 107 301 38 Flexibility: Low
Max RMSD: 3.7, Avg RMSD: 0.9
PDBFlex
90 % 107 301 43
70 % 107 301 55
50 % 128 468 27
40 % 128 471 38
30 % 128 471 57
Entity #2 | Chains: B
30S ribosomal protein S2 protein, length: 234 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name Structural variation in cluster
100 % 106 298 31
95 % 106 299 40 Flexibility: Low
Max RMSD: 9.2, Avg RMSD: 1.6
PDBFlex
90 % 106 299 45
70 % 106 299 58
50 % 127 452 34
40 % 127 458 46
30 % 127 458 64
Entity #20 | Chains: T
30S ribosomal protein S20 protein, length: 99 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name Structural variation in cluster
100 % 8 39 782
95 % 106 297 49 Flexibility: Low
Max RMSD: 1.4, Avg RMSD: 0.7
PDBFlex
90 % 106 297 54
70 % 106 297 65
50 % 106 297 94
40 % 106 297 115
30 % 106 297 129
Entity #21 | Chains: V
30S ribosomal protein Thx protein, length: 24 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name Structural variation in cluster
100 % 106 288 43
95 % 106 288 53 Flexibility: Low
Max RMSD: 1.2, Avg RMSD: 0.5
PDBFlex
90 % 106 288 59
70 % 106 288 71
50 % 106 288 99
40 % 106 288 121
30 % 106 288 131
Entity #22 | Chains: W
mRNA A-site fragment rna, length: 6 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
Entity #23 | Chains: X
tRNA ASL human mitochondrial Met rna, length: 17 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
Entity #3 | Chains: C
30S ribosomal protein S3 protein, length: 206 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name Structural variation in cluster
100 % 12 47 610
95 % 12 47 750 Flexibility: Low
Max RMSD: 0.8, Avg RMSD: 0.6
PDBFlex
90 % 12 47 776
70 % 12 47 827
50 % 29 127 306
40 % 29 133 322
30 % 29 133 330
Entity #4 | Chains: D
30S ribosomal protein S4 protein, length: 208 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name Structural variation in cluster
100 % 106 299 30
95 % 106 299 39 Flexibility: Low
Max RMSD: 1.6, Avg RMSD: 0.5
PDBFlex
90 % 106 299 44
70 % 106 299 57
50 % 127 462 29
40 % 127 468 40
30 % 127 468 60
Entity #5 | Chains: E
30S ribosomal protein S5 protein, length: 150 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name Structural variation in cluster
100 % 106 298 35
95 % 106 298 44 Flexibility: Low
Max RMSD: 4.8, Avg RMSD: 0.6
PDBFlex
90 % 106 298 49
70 % 106 298 61
50 % 128 463 31
40 % 128 463 44
30 % 128 465 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 % 108 303 27
95 % 114 309 34 Flexibility: Low
Max RMSD: 2.9, Avg RMSD: 0.9
PDBFlex
90 % 114 309 38
70 % 114 309 49
50 % 114 309 89
40 % 114 309 110
30 % 133 398 89
Entity #7 | Chains: G
30S ribosomal protein S7 protein, length: 155 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name Structural variation in cluster
100 % 107 303 28
95 % 107 303 37 Flexibility: Low
Max RMSD: 4.2, Avg RMSD: 0.8
PDBFlex
90 % 107 303 41
70 % 107 303 53
50 % 126 401 62
40 % 126 407 71
30 % 126 407 86
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 % 107 298 34
95 % 107 298 42 Flexibility: No
Max RMSD: 1.3, Avg RMSD: 0.4
PDBFlex
90 % 107 302 42
70 % 107 302 54
50 % 130 467 26
40 % 146 614 18
30 % 146 614 32
Entity #9 | Chains: I
30S ribosomal protein S9 protein, length: 127 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name Structural variation in cluster
100 % 12 96 231
95 % 106 298 46 Flexibility: Low
Max RMSD: 1.5, Avg RMSD: 0.7
PDBFlex
90 % 106 298 51
70 % 106 298 63
50 % 127 456 33
40 % 127 457 47
30 % 141 596 36

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