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 % 96 270 38
95 % 96 271 53 Flexibility: Low
Max RMSD: 2.0, Avg RMSD: 1.1
PDBFlex
90 % 96 271 57
70 % 96 271 69
50 % 123 432 26
40 % 123 432 40
30 % 137 545 34
Entity #11 | Chains: K
30S ribosomal protein S11 protein, length: 119 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 96 272 35
95 % 96 272 49
90 % 96 272 53
70 % 96 272 65
50 % 117 426 33
40 % 133 557 19
30 % 133 557 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 % 60 218 54
95 % 96 279 39 Flexibility: Low
Max RMSD: 1.2, Avg RMSD: 0.7
PDBFlex
90 % 96 279 44
70 % 117 430 18
50 % 117 443 24
40 % 117 443 38
30 % 117 443 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 % 96 273 33
95 % 96 273 47 Flexibility: Low
Max RMSD: 2.4, Avg RMSD: 0.7
PDBFlex
90 % 96 273 51
70 % 96 273 62
50 % 118 430 32
40 % 118 430 45
30 % 132 546 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 % 96 271 36
95 % 96 271 55 Flexibility: Low
Max RMSD: 2.1, Avg RMSD: 0.9
PDBFlex
90 % 96 271 59
70 % 96 284 54
50 % 96 284 92
40 % 96 284 115
30 % 96 284 124
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 % 96 275 30
95 % 100 280 38 Flexibility: Low
Max RMSD: 1.3, Avg RMSD: 0.5
PDBFlex
90 % 100 280 43
70 % 100 280 55
50 % 124 439 25
40 % 124 444 37
30 % 124 444 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 % 96 267 41
95 % 96 272 51 Flexibility: No
Max RMSD: 1.3, Avg RMSD: 0.4
PDBFlex
90 % 96 272 55
70 % 96 272 67
50 % 96 282 93
40 % 96 282 116
30 % 118 423 65
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 87 267
95 % 96 266 56 Flexibility: Low
Max RMSD: 1.9, Avg RMSD: 0.6
PDBFlex
90 % 96 270 60
70 % 96 270 70
50 % 96 270 97
40 % 96 270 120
30 % 96 270 128
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 % 1 7 5904
95 % 9 37 891 Flexibility: Low
Max RMSD: 1.3, Avg RMSD: 0.7
PDBFlex
90 % 9 37 924
70 % 9 37 958
50 % 9 37 1003
40 % 9 37 1027
30 % 9 37 1006
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 % 97 275 29
95 % 97 275 43 Flexibility: Low
Max RMSD: 3.7, Avg RMSD: 0.9
PDBFlex
90 % 97 275 48
70 % 97 275 59
50 % 118 432 29
40 % 118 435 41
30 % 118 435 59
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 % 96 272 31
95 % 96 273 44 Flexibility: Low
Max RMSD: 9.2, Avg RMSD: 1.5
PDBFlex
90 % 96 273 49
70 % 96 273 60
50 % 117 419 35
40 % 117 424 46
30 % 117 424 63
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 51 540
95 % 96 271 52 Flexibility: Low
Max RMSD: 1.4, Avg RMSD: 0.7
PDBFlex
90 % 96 271 56
70 % 96 271 68
50 % 96 271 96
40 % 96 271 119
30 % 96 271 127
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 % 96 262 43
95 % 96 262 59 Flexibility: Low
Max RMSD: 1.2, Avg RMSD: 0.5
PDBFlex
90 % 96 262 63
70 % 96 262 75
50 % 96 262 102
40 % 96 262 125
30 % 96 262 133
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 % 9 36 680
95 % 9 36 919 Flexibility: Low
Max RMSD: 0.8, Avg RMSD: 0.6
PDBFlex
90 % 9 36 952
70 % 9 36 985
50 % 26 109 334
40 % 26 114 335
30 % 26 114 345
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 % 96 265 42
95 % 96 273 45 Flexibility: Low
Max RMSD: 1.6, Avg RMSD: 0.5
PDBFlex
90 % 96 273 50
70 % 96 273 61
50 % 117 427 30
40 % 117 432 43
30 % 117 432 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 % 96 272 34
95 % 96 272 48 Flexibility: Low
Max RMSD: 4.8, Avg RMSD: 0.6
PDBFlex
90 % 96 272 52
70 % 96 272 63
50 % 118 427 31
40 % 118 427 44
30 % 118 429 62
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 % 98 277 27
95 % 104 283 37 Flexibility: Low
Max RMSD: 2.8, Avg RMSD: 0.8
PDBFlex
90 % 104 283 42
70 % 104 283 52
50 % 104 283 91
40 % 104 283 114
30 % 123 366 94
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 % 97 276 28
95 % 97 277 40 Flexibility: Low
Max RMSD: 2.2, Avg RMSD: 0.8
PDBFlex
90 % 97 277 45
70 % 97 277 56
50 % 116 367 66
40 % 116 372 84
30 % 116 372 96
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 % 97 272 32
95 % 97 272 46 Flexibility: No
Max RMSD: 1.3, Avg RMSD: 0.4
PDBFlex
90 % 97 276 46
70 % 97 276 57
50 % 120 432 28
40 % 121 438 39
30 % 136 562 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 91 229
95 % 96 272 50 Flexibility: Low
Max RMSD: 1.5, Avg RMSD: 0.8
PDBFlex
90 % 96 272 54
70 % 96 272 66
50 % 117 421 34
40 % 117 421 47
30 % 131 546 35

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