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 % 106 312 37
95 % 106 312 50 Flexibility: Low
Max RMSD: 2.1, Avg RMSD: 1.1
PDBFlex
90 % 106 312 56
70 % 106 312 66
50 % 133 497 21
40 % 147 625 22
30 % 147 627 35
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 % 106 313 34
95 % 106 313 47 Flexibility: Low
Max RMSD: 1.9, Avg RMSD: 0.7
PDBFlex
90 % 106 313 52
70 % 106 313 64
50 % 127 491 29
40 % 143 630 21
30 % 143 630 34
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 % 90 280 47
95 % 106 320 38 Flexibility: Low
Max RMSD: 1.2, Avg RMSD: 0.7
PDBFlex
90 % 106 320 43
70 % 127 505 14
50 % 127 508 20
40 % 127 508 34
30 % 127 508 53
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 % 106 314 31
95 % 106 314 43 Flexibility: Low
Max RMSD: 2.4, Avg RMSD: 0.7
PDBFlex
90 % 106 314 49
70 % 106 314 61
50 % 128 495 28
40 % 128 495 39
30 % 142 631 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 % 106 312 36
95 % 106 312 49 Flexibility: Low
Max RMSD: 2.1, Avg RMSD: 0.8
PDBFlex
90 % 106 312 54
70 % 106 319 54
50 % 106 330 90
40 % 106 330 108
30 % 106 330 120
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 % 107 318 25
95 % 110 321 37 Flexibility: Low
Max RMSD: 1.3, Avg RMSD: 0.5
PDBFlex
90 % 110 321 42
70 % 110 321 53
50 % 134 503 22
40 % 134 508 33
30 % 134 508 52
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 % 106 308 38
95 % 106 313 45 Flexibility: No
Max RMSD: 1.3, Avg RMSD: 0.5
PDBFlex
90 % 106 313 50
70 % 106 313 62
50 % 106 325 93
40 % 128 488 43
30 % 128 488 61
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 29 1570
95 % 106 310 53 Flexibility: Low
Max RMSD: 2.6, Avg RMSD: 0.7
PDBFlex
90 % 106 310 58
70 % 106 310 68
50 % 106 310 98
40 % 106 310 116
30 % 106 310 128
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 52 544
95 % 12 52 679 Flexibility: Low
Max RMSD: 1.3, Avg RMSD: 0.7
PDBFlex
90 % 12 52 703
70 % 12 52 749
50 % 12 52 806
40 % 12 52 840
30 % 12 52 846
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 % 107 316 28
95 % 107 316 40 Flexibility: Low
Max RMSD: 3.7, Avg RMSD: 0.9
PDBFlex
90 % 107 316 46
70 % 128 491 16
50 % 128 497 25
40 % 128 500 35
30 % 128 500 56
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 % 106 313 30
95 % 106 314 42 Flexibility: Low
Max RMSD: 9.2, Avg RMSD: 1.6
PDBFlex
90 % 106 314 48
70 % 106 314 60
50 % 127 477 34
40 % 127 483 45
30 % 127 483 62
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 45 691
95 % 106 312 51 Flexibility: Low
Max RMSD: 1.4, Avg RMSD: 0.7
PDBFlex
90 % 106 312 57
70 % 106 312 67
50 % 106 312 97
40 % 106 312 115
30 % 106 312 126
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 % 106 302 41
95 % 106 302 55 Flexibility: Low
Max RMSD: 1.2, Avg RMSD: 0.5
PDBFlex
90 % 106 302 59
70 % 106 302 71
50 % 106 302 100
40 % 106 302 119
30 % 106 302 132
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 53 528
95 % 12 53 659 Flexibility: Low
Max RMSD: 0.8, Avg RMSD: 0.6
PDBFlex
90 % 12 53 683
70 % 12 53 735
50 % 29 143 270
40 % 29 149 288
30 % 29 149 301
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 % 106 314 29
95 % 106 314 41 Flexibility: Low
Max RMSD: 1.6, Avg RMSD: 0.5
PDBFlex
90 % 106 314 47
70 % 106 314 59
50 % 127 491 27
40 % 127 497 37
30 % 127 497 58
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 % 106 313 33
95 % 106 313 46 Flexibility: Low
Max RMSD: 4.8, Avg RMSD: 0.6
PDBFlex
90 % 106 313 51
70 % 106 313 63
50 % 128 487 31
40 % 128 487 41
30 % 128 489 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 % 108 318 26
95 % 114 324 34 Flexibility: Low
Max RMSD: 2.9, Avg RMSD: 0.9
PDBFlex
90 % 114 324 39
70 % 114 324 51
50 % 114 324 91
40 % 114 324 109
30 % 133 427 81
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 % 107 318 27
95 % 107 318 39 Flexibility: Low
Max RMSD: 4.2, Avg RMSD: 0.8
PDBFlex
90 % 107 318 44
70 % 107 318 55
50 % 126 430 51
40 % 126 436 64
30 % 126 436 78
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 % 107 313 32
95 % 107 313 44 Flexibility: No
Max RMSD: 1.3, Avg RMSD: 0.4
PDBFlex
90 % 107 317 45
70 % 107 317 57
50 % 130 496 24
40 % 146 647 19
30 % 146 647 33
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 96 241
95 % 106 313 48 Flexibility: Low
Max RMSD: 1.5, Avg RMSD: 0.7
PDBFlex
90 % 106 313 53
70 % 106 313 65
50 % 127 482 33
40 % 127 482 46
30 % 141 629 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