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 % 106 303 39
95 % 106 303 50 Flexibility: Low
Max RMSD: 2.1, Avg RMSD: 1.1
PDBFlex
90 % 106 303 54
70 % 106 303 65
50 % 133 484 24
40 % 147 608 22
30 % 147 610 36
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 % 106 304 37
95 % 106 304 47 Flexibility: Low
Max RMSD: 1.9, Avg RMSD: 0.7
PDBFlex
90 % 106 304 51
70 % 106 304 63
50 % 127 478 31
40 % 143 617 21
30 % 143 617 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 % 90 274 47
95 % 106 311 38 Flexibility: Low
Max RMSD: 1.2, Avg RMSD: 0.7
PDBFlex
90 % 106 311 42
70 % 127 492 15
50 % 127 495 22
40 % 127 495 36
30 % 127 495 57
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 % 106 305 33
95 % 106 305 43 Flexibility: Low
Max RMSD: 2.4, Avg RMSD: 0.7
PDBFlex
90 % 106 305 48
70 % 106 305 59
50 % 128 482 30
40 % 128 482 41
30 % 142 614 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 % 106 303 38
95 % 106 303 49 Flexibility: Low
Max RMSD: 2.1, Avg RMSD: 0.8
PDBFlex
90 % 106 303 53
70 % 106 307 56
50 % 106 318 91
40 % 106 318 111
30 % 106 318 123
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 % 107 309 27
95 % 110 312 37 Flexibility: Low
Max RMSD: 1.3, Avg RMSD: 0.5
PDBFlex
90 % 110 312 41
70 % 110 312 52
50 % 134 490 25
40 % 134 495 35
30 % 134 495 56
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 % 106 299 41
95 % 106 304 45 Flexibility: No
Max RMSD: 1.3, Avg RMSD: 0.5
PDBFlex
90 % 106 304 49
70 % 106 304 61
50 % 106 316 93
40 % 128 479 44
30 % 128 479 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 29 1546
95 % 106 301 52 Flexibility: Low
Max RMSD: 2.6, Avg RMSD: 0.7
PDBFlex
90 % 106 301 56
70 % 106 301 68
50 % 106 301 98
40 % 106 301 117
30 % 106 301 130
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 52 535
95 % 12 52 673 Flexibility: Low
Max RMSD: 1.3, Avg RMSD: 0.7
PDBFlex
90 % 12 52 696
70 % 12 52 742
50 % 12 52 799
40 % 12 52 833
30 % 12 52 838
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 % 107 307 30
95 % 107 307 40 Flexibility: Low
Max RMSD: 3.7, Avg RMSD: 0.9
PDBFlex
90 % 107 307 45
70 % 107 307 55
50 % 128 484 28
40 % 128 487 39
30 % 128 487 58
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 % 106 304 32
95 % 106 305 42 Flexibility: Low
Max RMSD: 9.2, Avg RMSD: 1.6
PDBFlex
90 % 106 305 47
70 % 106 305 58
50 % 127 467 34
40 % 127 473 46
30 % 127 473 65
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 42 759
95 % 106 303 51 Flexibility: Low
Max RMSD: 1.4, Avg RMSD: 0.7
PDBFlex
90 % 106 303 55
70 % 106 303 66
50 % 106 303 96
40 % 106 303 116
30 % 106 303 127
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 % 106 294 44
95 % 106 294 53 Flexibility: Low
Max RMSD: 1.2, Avg RMSD: 0.5
PDBFlex
90 % 106 294 59
70 % 106 294 72
50 % 106 294 100
40 % 106 294 122
30 % 106 294 132
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 50 575
95 % 12 50 718 Flexibility: Low
Max RMSD: 0.8, Avg RMSD: 0.6
PDBFlex
90 % 12 50 749
70 % 12 50 795
50 % 29 139 277
40 % 29 145 292
30 % 29 145 306
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 % 106 305 31
95 % 106 305 41 Flexibility: Low
Max RMSD: 1.6, Avg RMSD: 0.5
PDBFlex
90 % 106 305 46
70 % 106 305 57
50 % 127 478 29
40 % 127 484 40
30 % 127 484 59
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 % 106 304 36
95 % 106 304 46 Flexibility: Low
Max RMSD: 4.8, Avg RMSD: 0.6
PDBFlex
90 % 106 304 50
70 % 106 304 62
50 % 128 478 32
40 % 128 478 42
30 % 128 480 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 % 108 309 28
95 % 114 315 36 Flexibility: Low
Max RMSD: 2.9, Avg RMSD: 0.9
PDBFlex
90 % 114 315 40
70 % 114 315 51
50 % 114 315 92
40 % 114 315 112
30 % 133 414 87
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 % 107 309 29
95 % 107 309 39 Flexibility: Low
Max RMSD: 4.2, Avg RMSD: 0.8
PDBFlex
90 % 107 309 43
70 % 107 309 53
50 % 126 417 60
40 % 126 423 64
30 % 126 423 80
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 % 107 304 34
95 % 107 304 44 Flexibility: No
Max RMSD: 1.3, Avg RMSD: 0.4
PDBFlex
90 % 107 308 44
70 % 107 308 54
50 % 130 483 27
40 % 146 630 19
30 % 146 630 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 96 236
95 % 106 304 48 Flexibility: Low
Max RMSD: 1.5, Avg RMSD: 0.7
PDBFlex
90 % 106 304 52
70 % 106 304 64
50 % 127 471 33
40 % 127 472 47
30 % 141 612 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