Sequence Similarity Clusters for the Entities in PDB 1NKW

Entity #1 | Chains: 0
23S ribosomal RNA rna, length: 2880 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
Entity #10 | Chains: H
50S ribosomal protein L13 protein, length: 174 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name Structural variation in cluster
100 % 3 19 2629
95 % 3 19 3282 Flexibility: Low
Max RMSD: 1.9, Avg RMSD: 1.2
PDBFlex
90 % 3 19 3326
70 % 3 19 3300
50 % 3 19 3225
40 % 3 19 3138
30 % 3 19 2948
Entity #11 | Chains: I
50S ribosomal protein L14 protein, length: 134 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name Structural variation in cluster
100 % 4 24 1574
95 % 4 24 2094 Flexibility: Low
Max RMSD: 1.6, Avg RMSD: 0.8
PDBFlex
90 % 4 24 2146
70 % 101 211 84
50 % 129 359 52
40 % 222 543 20
30 % 222 543 33
Entity #12 | Chains: J
50S ribosomal protein L15 protein, length: 156 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name Structural variation in cluster
100 % 4 24 1569
95 % 4 24 2083 Flexibility: Low
Max RMSD: 8.4, Avg RMSD: 2.9
PDBFlex
90 % 4 24 2132
70 % 4 24 2127
50 % 128 342 63
40 % 128 342 83
30 % 221 523 37
Entity #13 | Chains: K
50S ribosomal protein L16 protein, length: 142 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name Structural variation in cluster
100 % 4 27 1323
95 % 4 27 1788 Flexibility: Low
Max RMSD: 5.2, Avg RMSD: 2.5
PDBFlex
90 % 4 27 1825
70 % 95 182 93
50 % 128 350 55
40 % 128 350 71
30 % 128 350 83
Entity #14 | Chains: L
50S ribosomal protein L17 protein, length: 116 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name Structural variation in cluster
100 % 4 24 1585
95 % 4 24 2103 Flexibility: Low
Max RMSD: 1.7, Avg RMSD: 0.9
PDBFlex
90 % 4 24 2156
70 % 4 24 2149
50 % 124 322 68
40 % 129 347 68
30 % 129 349 82
Entity #15 | Chains: M
50S ribosomal protein L18 protein, length: 114 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name Structural variation in cluster
100 % 3 22 1718
95 % 4 24 2104 Flexibility: Low
Max RMSD: 2.8, Avg RMSD: 1.6
PDBFlex
90 % 4 24 2157
70 % 4 24 2150
50 % 128 344 62
40 % 128 344 80
30 % 128 344 92
Entity #16 | Chains: N
50S ribosomal protein L19 protein, length: 166 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name Structural variation in cluster
100 % 3 19 2633
95 % 3 19 3285 Flexibility: Medium
Max RMSD: 7.0, Avg RMSD: 3.1
PDBFlex
90 % 3 19 3329
70 % 3 19 3305
50 % 3 19 3229
40 % 3 19 3140
30 % 3 19 2951
Entity #17 | Chains: O
50S ribosomal protein L20 protein, length: 118 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name Structural variation in cluster
100 % 4 28 1293
95 % 4 28 1745 Flexibility: Low
Max RMSD: 1.4, Avg RMSD: 0.8
PDBFlex
90 % 4 28 1780
70 % 4 28 1803
50 % 129 347 56
40 % 129 354 67
30 % 129 354 81
Entity #18 | Chains: P
50S ribosomal protein L21 protein, length: 100 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name Structural variation in cluster
100 % 4 28 1297
95 % 4 28 1749 Flexibility: Medium
Max RMSD: 7.9, Avg RMSD: 3.6
PDBFlex
90 % 4 28 1784
70 % 4 28 1808
50 % 100 201 123
40 % 128 342 84
30 % 128 342 96
Entity #19 | Chains: Q
50S ribosomal protein L22 protein, length: 134 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name Structural variation in cluster
100 % 4 28 1289
95 % 4 30 1616 Flexibility: Low
Max RMSD: 2.5, Avg RMSD: 1.1
PDBFlex
90 % 4 30 1652
70 % 4 30 1665
50 % 4 30 1700
40 % 4 30 1704
30 % 4 30 1669
Entity #2 | Chains: 9
5S ribosomal RNA rna, length: 124 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
Entity #20 | Chains: R
50S ribosomal protein L23 protein, length: 95 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 4 26 1422
95 % 4 26 1911
90 % 4 26 1956
70 % 4 26 1979
50 % 95 181 132
40 % 128 348 74
30 % 195 426 59
Entity #21 | Chains: S
50S ribosomal protein L24 protein, length: 115 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 4 25 1466
95 % 4 25 1980
90 % 4 25 2027
70 % 4 25 2036
50 % 128 345 61
40 % 128 347 77
30 % 128 347 88
Entity #22 | Chains: T
general stress protein CTC protein, length: 253 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name Structural variation in cluster
100 % 3 25 1758
95 % 3 25 2307 Flexibility: Low
Max RMSD: 6.5, Avg RMSD: 1.7
PDBFlex
90 % 3 25 2369
70 % 3 25 2365
50 % 3 25 2349
40 % 3 25 2334
30 % 3 25 2237
Entity #23 | Chains: U
50S ribosomal protein L27 protein, length: 91 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name Structural variation in cluster
100 % 4 29 1233
95 % 4 29 1659 Flexibility: Medium
Max RMSD: 11.9, Avg RMSD: 4.7
PDBFlex
90 % 4 29 1694
70 % 33 169 169
50 % 130 346 57
40 % 130 346 75
30 % 130 346 86
Entity #24 | Chains: W
50S ribosomal protein L29 protein, length: 67 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name Structural variation in cluster
100 % 4 26 1426
95 % 4 26 1916 Flexibility: Low
Max RMSD: 2.8, Avg RMSD: 1.5
PDBFlex
90 % 4 26 1961
70 % 4 26 1985
50 % 4 26 1989
40 % 4 26 1982
30 % 195 413 64
Entity #25 | Chains: X
50S ribosomal protein L30 protein, length: 55 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name Structural variation in cluster
100 % 4 24 1599
95 % 4 24 2124 Flexibility: Low
Max RMSD: 1.8, Avg RMSD: 0.9
PDBFlex
90 % 4 24 2175
70 % 4 24 2164
50 % 37 185 188
40 % 129 348 72
30 % 129 348 85
Entity #26 | Chains: Y
50S ribosomal protein L31 protein, length: 73 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name Structural variation in cluster
100 % 1 12 3451
95 % 1 12 4229 Flexibility: No
Max RMSD: 0.5, Avg RMSD: 0.4
PDBFlex
90 % 1 12 4259
70 % 1 12 4193
50 % 91 204 128
40 % 91 215 142
30 % 91 215 157
Entity #27 | Chains: Z
50S ribosomal protein L32 protein, length: 60 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name Structural variation in cluster
100 % 4 34 1035
95 % 4 34 1422 Flexibility: Low
Max RMSD: 1.5, Avg RMSD: 0.9
PDBFlex
90 % 4 34 1445
70 % 4 34 1442
50 % 100 201 126
40 % 128 344 81
30 % 128 344 94
Entity #28 | Chains: 1
50S ribosomal protein L33 protein, length: 82 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 1 6 13970
95 % 1 6 13264
90 % 1 6 13052
70 % 1 6 12289
50 % 1 6 10961
40 % 1 6 9946
30 % 1 6 8666
Entity #29 | Chains: 2
50S ribosomal protein L34 protein, length: 47 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name Structural variation in cluster
100 % 4 28 1304
95 % 4 28 1755 Flexibility: Low
Max RMSD: 1.8, Avg RMSD: 1.1
PDBFlex
90 % 4 28 1790
70 % 32 164 171
50 % 37 187 187
40 % 37 187 203
30 % 37 187 216
Entity #3 | Chains: A
50S ribosomal protein L2 protein, length: 275 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name Structural variation in cluster
100 % 3 22 1683
95 % 4 24 2048 Flexibility: Low
Max RMSD: 7.5, Avg RMSD: 2.1
PDBFlex
90 % 4 24 2095
70 % 96 179 96
50 % 129 347 58
40 % 129 347 78
30 % 129 347 89
Entity #30 | Chains: 3
50S ribosomal protein L35 protein, length: 64 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name Structural variation in cluster
100 % 4 28 1303
95 % 4 28 1754 Flexibility: Low
Max RMSD: 3.7, Avg RMSD: 1.8
PDBFlex
90 % 4 28 1788
70 % 4 28 1813
50 % 96 183 130
40 % 129 340 86
30 % 129 340 97
Entity #31 | Chains: 4
50S ribosomal protein L36 protein, length: 36 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name Structural variation in cluster
100 % 3 22 1727
95 % 3 22 2276 Flexibility: Low
Max RMSD: 1.4, Avg RMSD: 1.0
PDBFlex
90 % 3 22 2340
70 % 64 156 149
50 % 92 296 86
40 % 92 296 106
30 % 92 296 120
Entity #4 | Chains: B
50S ribosomal protein L3 protein, length: 211 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name Structural variation in cluster
100 % 4 27 1318
95 % 4 27 1780 Flexibility: Low
Max RMSD: 2.7, Avg RMSD: 1.6
PDBFlex
90 % 4 27 1817
70 % 4 27 1841
50 % 134 351 60
40 % 134 354 73
30 % 134 355 84
Entity #5 | Chains: C
50S ribosomal protein L4 protein, length: 205 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name Structural variation in cluster
100 % 4 29 1224
95 % 4 29 1645 Flexibility: Low
Max RMSD: 2.2, Avg RMSD: 1.2
PDBFlex
90 % 4 29 1681
70 % 4 29 1704
50 % 96 184 129
40 % 130 348 76
30 % 130 348 87
Entity #6 | Chains: D
50S ribosomal protein L5 protein, length: 180 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 4 24 1562
95 % 4 24 2078
90 % 4 24 2127
70 % 96 179 94
50 % 133 347 59
40 % 133 347 79
30 % 133 347 90
Entity #7 | Chains: E
50S ribosomal protein L6 protein, length: 212 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name Structural variation in cluster
100 % 1 2 40792
95 % 1 2 31068 Flexibility: Low
Max RMSD: 0.7, Avg RMSD: 0.7
PDBFlex
90 % 1 2 29748
70 % 1 2 26626
50 % 1 2 22723
40 % 1 2 20002
30 % 1 2 16942
Entity #8 | Chains: F
50S ribosomal protein L9 protein, length: 146 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name Structural variation in cluster
100 % 1 5 15558
95 % 1 5 14583 Flexibility: No
Max RMSD: 0.6, Avg RMSD: 0.4
PDBFlex
90 % 1 5 14311
70 % 1 5 13445
50 % 79 130 179
40 % 105 269 110
30 % 105 277 121
Entity #9 | Chains: G
50S ribosomal protein L11 protein, length: 144 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name Structural variation in cluster
100 % 3 19 2066
95 % 4 21 2330 Flexibility: Low
Max RMSD: 3.8, Avg RMSD: 2.1
PDBFlex
90 % 4 21 2393
70 % 19 62 497
50 % 48 229 141
40 % 48 232 153
30 % 48 235 166

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.