4GKJ

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 AUG-codon in the A-site and paromomycin.


Sequence Similarity Clusters for the Entities in PDB 4GKJ

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 % 99 269 39
95 % 99 270 53 Flexibility: Low
Max RMSD: 2.1, Avg RMSD: 1.1
PDBFlex
90 % 99 270 58
70 % 99 270 69
50 % 127 428 26
40 % 127 428 38
30 % 141 535 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 % 99 271 35
95 % 99 271 49 Flexibility: Low
Max RMSD: 1.9, Avg RMSD: 0.7
PDBFlex
90 % 99 271 54
70 % 99 271 65
50 % 121 422 32
40 % 137 546 19
30 % 137 546 31
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 % 61 217 52
95 % 99 278 39 Flexibility: Low
Max RMSD: 1.2, Avg RMSD: 0.7
PDBFlex
90 % 99 278 44
70 % 121 426 18
50 % 121 439 24
40 % 121 439 36
30 % 121 439 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 % 99 272 33
95 % 99 272 46 Flexibility: Low
Max RMSD: 2.4, Avg RMSD: 0.7
PDBFlex
90 % 99 272 51
70 % 99 272 62
50 % 123 426 31
40 % 123 426 44
30 % 137 535 35
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 % 99 270 36
95 % 99 270 54 Flexibility: Low
Max RMSD: 2.1, Avg RMSD: 0.8
PDBFlex
90 % 99 270 59
70 % 99 283 53
50 % 99 283 91
40 % 99 283 112
30 % 99 283 124
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 % 99 274 30
95 % 103 279 38 Flexibility: Low
Max RMSD: 1.3, Avg RMSD: 0.5
PDBFlex
90 % 103 279 43
70 % 103 279 54
50 % 128 435 25
40 % 128 440 35
30 % 128 440 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 % 99 266 41
95 % 99 271 51 Flexibility: No
Max RMSD: 1.3, Avg RMSD: 0.5
PDBFlex
90 % 99 271 56
70 % 99 271 67
50 % 99 281 92
40 % 99 281 114
30 % 123 419 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 % 20 87 259
95 % 99 265 56 Flexibility: Low
Max RMSD: 1.9, Avg RMSD: 0.6
PDBFlex
90 % 99 269 60
70 % 99 269 70
50 % 99 269 95
40 % 99 269 117
30 % 99 269 128
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 % 2 7 5810
95 % 11 37 863 Flexibility: Low
Max RMSD: 1.3, Avg RMSD: 0.7
PDBFlex
90 % 11 37 896
70 % 11 37 936
50 % 11 37 990
40 % 11 37 1012
30 % 11 37 986
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 % 100 274 29
95 % 100 274 42 Flexibility: Low
Max RMSD: 3.7, Avg RMSD: 0.9
PDBFlex
90 % 100 274 48
70 % 100 274 58
50 % 122 428 28
40 % 122 431 40
30 % 122 431 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 % 99 271 31
95 % 99 272 43 Flexibility: Low
Max RMSD: 9.2, Avg RMSD: 1.5
PDBFlex
90 % 99 272 49
70 % 99 272 59
50 % 121 415 34
40 % 121 420 45
30 % 121 420 61
Entity #20 | Chains: T
30S ribosomal protein S20 protein, length: 99 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 9 51 527
95 % 99 270 52
90 % 99 270 57
70 % 99 270 68
50 % 99 270 94
40 % 99 270 116
30 % 99 270 127
Entity #21 | Chains: V
30S ribosomal protein Thx protein, length: 24 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 99 261 43
95 % 99 261 59
90 % 99 261 63
70 % 99 261 74
50 % 99 261 100
40 % 99 261 122
30 % 99 261 135
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 % 11 36 664
95 % 11 36 900 Flexibility: Low
Max RMSD: 0.8, Avg RMSD: 0.6
PDBFlex
90 % 11 36 935
70 % 11 36 970
50 % 29 106 322
40 % 29 111 323
30 % 29 111 333
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 % 99 264 42
95 % 99 272 44 Flexibility: Low
Max RMSD: 1.6, Avg RMSD: 0.5
PDBFlex
90 % 99 272 50
70 % 99 272 60
50 % 121 423 29
40 % 121 428 42
30 % 121 428 58
Entity #5 | Chains: E
30S ribosomal protein S5 protein, length: 150 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 99 271 34
95 % 99 271 48
90 % 99 271 53
70 % 99 271 64
50 % 122 423 30
40 % 122 423 43
30 % 122 425 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 % 101 276 27
95 % 107 282 37 Flexibility: Low
Max RMSD: 2.8, Avg RMSD: 0.8
PDBFlex
90 % 107 282 42
70 % 107 282 52
50 % 107 282 90
40 % 107 282 111
30 % 127 362 93
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 % 100 275 28
95 % 100 276 41 Flexibility: Low
Max RMSD: 4.2, Avg RMSD: 0.9
PDBFlex
90 % 100 276 46
70 % 100 276 56
50 % 121 363 66
40 % 121 368 82
30 % 121 368 95
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 % 100 271 32
95 % 100 271 45 Flexibility: No
Max RMSD: 1.3, Avg RMSD: 0.4
PDBFlex
90 % 100 275 47
70 % 100 275 57
50 % 124 428 27
40 % 125 434 37
30 % 140 551 30
Entity #9 | Chains: I
30S ribosomal protein S9 protein, length: 127 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 13 91 220
95 % 99 271 50
90 % 99 271 55
70 % 99 271 66
50 % 121 417 33
40 % 121 417 46
30 % 135 535 34

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.