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 % 111 333 36
95 % 111 334 59 Flexibility: Low
Max RMSD: 2.2, Avg RMSD: 1.1
PDBFlex
90 % 111 334 64
70 % 111 334 75
50 % 134 549 26
40 % 134 549 34
30 % 134 586 32
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 % 111 335 33
95 % 111 335 53 Flexibility: Low
Max RMSD: 1.9, Avg RMSD: 0.7
PDBFlex
90 % 111 335 61
70 % 111 335 73
50 % 133 543 29
40 % 133 543 38
30 % 133 543 41
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 % 13 104 279
95 % 111 342 47 Flexibility: Low
Max RMSD: 1.2, Avg RMSD: 0.7
PDBFlex
90 % 111 342 52
70 % 134 547 17
50 % 134 565 22
40 % 134 565 28
30 % 134 565 33
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 % 111 336 30
95 % 111 336 52 Flexibility: Low
Max RMSD: 2.4, Avg RMSD: 0.7
PDBFlex
90 % 111 336 57
70 % 111 336 69
50 % 134 549 27
40 % 134 552 35
30 % 134 552 38
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 % 111 334 35
95 % 111 334 57 Flexibility: Low
Max RMSD: 2.1, Avg RMSD: 0.8
PDBFlex
90 % 111 334 62
70 % 111 355 55
50 % 111 355 89
40 % 111 355 104
30 % 111 355 103
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 % 111 338 29
95 % 115 343 44 Flexibility: Low
Max RMSD: 1.3, Avg RMSD: 0.5
PDBFlex
90 % 115 343 48
70 % 115 343 59
50 % 140 561 23
40 % 140 561 30
30 % 140 561 34
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 % 111 330 37
95 % 111 335 55 Flexibility: No
Max RMSD: 1.3, Avg RMSD: 0.5
PDBFlex
90 % 111 335 59
70 % 111 335 70
50 % 111 335 94
40 % 111 335 111
30 % 111 335 113
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 % 18 101 332
95 % 111 328 60 Flexibility: Low
Max RMSD: 2.0, Avg RMSD: 0.6
PDBFlex
90 % 111 332 65
70 % 111 332 76
50 % 111 332 96
40 % 111 332 113
30 % 111 332 116
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 % 1 8 6044
95 % 13 55 779 Flexibility: Low
Max RMSD: 1.3, Avg RMSD: 0.6
PDBFlex
90 % 13 55 808
70 % 13 55 844
50 % 13 55 879
40 % 13 55 911
30 % 13 55 956
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 % 9 45 746
95 % 9 45 1015 Flexibility: Low
Max RMSD: 1.4, Avg RMSD: 0.8
PDBFlex
90 % 9 45 1061
70 % 112 338 64
50 % 134 550 25
40 % 134 550 33
30 % 134 550 37
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 % 111 334 32
95 % 111 336 49 Flexibility: Low
Max RMSD: 9.2, Avg RMSD: 1.5
PDBFlex
90 % 111 336 55
70 % 111 336 66
50 % 133 541 30
40 % 133 547 36
30 % 133 547 39
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 56 588
95 % 111 334 58 Flexibility: Low
Max RMSD: 1.4, Avg RMSD: 0.7
PDBFlex
90 % 111 334 63
70 % 111 334 74
50 % 111 334 95
40 % 111 334 112
30 % 111 334 114
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 % 10 32 1090
95 % 10 32 1474 Flexibility: No
Max RMSD: 0.7, Avg RMSD: 0.4
PDBFlex
90 % 10 32 1507
70 % 10 32 1541
50 % 10 32 1576
40 % 10 32 1623
30 % 10 32 1652
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 % 13 56 564
95 % 13 56 768 Flexibility: Low
Max RMSD: 0.9, Avg RMSD: 0.6
PDBFlex
90 % 13 56 795
70 % 13 56 830
50 % 31 171 289
40 % 31 171 299
30 % 31 177 309
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 % 111 328 38
95 % 111 336 50 Flexibility: Low
Max RMSD: 1.6, Avg RMSD: 0.5
PDBFlex
90 % 111 336 56
70 % 111 336 67
50 % 133 525 33
40 % 133 555 31
30 % 133 555 35
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 % 111 335 34
95 % 111 335 54 Flexibility: Low
Max RMSD: 4.8, Avg RMSD: 0.6
PDBFlex
90 % 111 335 58
70 % 111 335 71
50 % 134 545 28
40 % 134 545 37
30 % 134 545 40
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 % 113 340 26
95 % 121 348 40 Flexibility: Low
Max RMSD: 2.9, Avg RMSD: 0.8
PDBFlex
90 % 121 348 45
70 % 121 348 57
50 % 121 348 90
40 % 121 348 106
30 % 121 348 106
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 % 112 339 27
95 % 112 340 48 Flexibility: Low
Max RMSD: 4.2, Avg RMSD: 0.8
PDBFlex
90 % 112 340 54
70 % 112 338 65
50 % 133 479 52
40 % 133 485 68
30 % 133 485 70
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 % 112 335 31
95 % 112 335 51 Flexibility: No
Max RMSD: 1.3, Avg RMSD: 0.4
PDBFlex
90 % 112 339 53
70 % 112 339 62
50 % 113 364 86
40 % 136 560 29
30 % 151 763 22
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 % 12 101 283
95 % 111 335 56 Flexibility: Low
Max RMSD: 1.5, Avg RMSD: 0.7
PDBFlex
90 % 111 335 60
70 % 111 335 72
50 % 133 538 31
40 % 133 538 39
30 % 133 538 44

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