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 2693
95 % 3 19 3338 Flexibility: Low
Max RMSD: 1.9, Avg RMSD: 1.3
PDBFlex
90 % 3 19 3385
70 % 3 19 3349
50 % 3 19 3262
40 % 3 19 3172
30 % 3 19 2977
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 1604
95 % 4 24 2124 Flexibility: Low
Max RMSD: 1.3, Avg RMSD: 0.8
PDBFlex
90 % 4 24 2176
70 % 102 212 88
50 % 130 363 51
40 % 225 552 20
30 % 225 552 36
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 1599
95 % 4 24 2114 Flexibility: Low
Max RMSD: 3.4, Avg RMSD: 1.9
PDBFlex
90 % 4 24 2164
70 % 4 24 2160
50 % 129 346 65
40 % 129 346 85
30 % 224 532 39
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 1355
95 % 4 27 1816 Flexibility: Low
Max RMSD: 5.2, Avg RMSD: 2.7
PDBFlex
90 % 4 27 1852
70 % 96 183 99
50 % 129 354 56
40 % 129 354 72
30 % 129 354 84
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 1615
95 % 4 24 2133 Flexibility: Low
Max RMSD: 1.7, Avg RMSD: 0.9
PDBFlex
90 % 4 24 2186
70 % 4 24 2180
50 % 125 326 68
40 % 130 351 68
30 % 130 353 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 1751
95 % 4 24 2134 Flexibility: Low
Max RMSD: 2.8, Avg RMSD: 1.5
PDBFlex
90 % 4 24 2187
70 % 4 24 2181
50 % 129 348 64
40 % 129 348 82
30 % 129 348 93
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 2697
95 % 3 19 3341 Flexibility: Medium
Max RMSD: 6.7, Avg RMSD: 3.3
PDBFlex
90 % 3 19 3388
70 % 3 19 3354
50 % 3 19 3266
40 % 3 19 3174
30 % 3 19 2980
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 1323
95 % 4 28 1767 Flexibility: Low
Max RMSD: 1.4, Avg RMSD: 0.8
PDBFlex
90 % 4 28 1804
70 % 4 28 1829
50 % 130 351 57
40 % 130 358 65
30 % 130 358 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 1327
95 % 4 28 1772 Flexibility: Medium
Max RMSD: 7.9, Avg RMSD: 3.5
PDBFlex
90 % 4 28 1809
70 % 4 28 1834
50 % 101 202 124
40 % 129 346 86
30 % 129 346 97
Entity #19 | Chains: Q
50S ribosomal protein L22 protein, length: 134 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 4 28 1319
95 % 4 30 1637
90 % 4 30 1673
70 % 4 30 1687
50 % 4 30 1725
40 % 4 30 1730
30 % 4 30 1691
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 1452
95 % 4 26 1936
90 % 4 26 1982
70 % 4 26 2007
50 % 96 182 139
40 % 129 352 75
30 % 196 430 61
Entity #21 | Chains: S
50S ribosomal protein L24 protein, length: 115 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name Structural variation in cluster
100 % 4 25 1496
95 % 4 25 2008 Flexibility: Low
Max RMSD: 3.3, Avg RMSD: 1.6
PDBFlex
90 % 4 25 2054
70 % 4 25 2066
50 % 129 349 63
40 % 129 351 78
30 % 129 351 89
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 1792
95 % 3 25 2343 Flexibility: Low
Max RMSD: 6.5, Avg RMSD: 1.8
PDBFlex
90 % 3 25 2408
70 % 3 25 2405
50 % 3 25 2386
40 % 3 25 2370
30 % 3 25 2265
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 1261
95 % 4 29 1680 Flexibility: Medium
Max RMSD: 11.9, Avg RMSD: 5.1
PDBFlex
90 % 4 29 1717
70 % 33 172 172
50 % 131 350 58
40 % 131 350 76
30 % 131 350 87
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 1457
95 % 4 26 1941 Flexibility: Low
Max RMSD: 2.8, Avg RMSD: 1.5
PDBFlex
90 % 4 26 1987
70 % 4 26 2013
50 % 4 26 2023
40 % 4 26 2015
30 % 196 417 67
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 1629
95 % 4 24 2154 Flexibility: Low
Max RMSD: 1.8, Avg RMSD: 0.9
PDBFlex
90 % 4 24 2205
70 % 4 24 2195
50 % 37 188 191
40 % 130 352 73
30 % 130 352 86
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 3519
95 % 1 12 4298 Flexibility: No
Max RMSD: 0.5, Avg RMSD: 0.4
PDBFlex
90 % 1 12 4331
70 % 1 12 4253
50 % 92 208 135
40 % 92 219 147
30 % 92 219 158
Entity #27 | Chains: Z
50S ribosomal protein L32 protein, length: 60 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 4 34 1060
95 % 4 34 1442
90 % 4 34 1463
70 % 4 34 1462
50 % 101 202 132
40 % 129 348 83
30 % 129 348 95
Entity #28 | Chains: 1
50S ribosomal protein L33 protein, length: 82 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name Structural variation in cluster
100 % 1 6 14162
95 % 1 6 13429 Flexibility: Low
Max RMSD: 0.5, Avg RMSD: 0.5
PDBFlex
90 % 1 6 13211
70 % 1 6 12426
50 % 1 6 11082
40 % 1 6 10053
30 % 1 6 8764
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 1334
95 % 4 28 1778 Flexibility: Low
Max RMSD: 1.6, Avg RMSD: 1.0
PDBFlex
90 % 4 28 1815
70 % 32 167 173
50 % 37 190 190
40 % 37 190 205
30 % 37 190 216
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 1714
95 % 4 24 2077 Flexibility: Low
Max RMSD: 7.5, Avg RMSD: 2.3
PDBFlex
90 % 4 24 2125
70 % 97 180 101
50 % 130 351 60
40 % 130 351 79
30 % 130 351 90
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 1333
95 % 4 28 1777 Flexibility: Low
Max RMSD: 3.7, Avg RMSD: 1.7
PDBFlex
90 % 4 28 1813
70 % 4 28 1839
50 % 97 184 138
40 % 130 344 87
30 % 130 344 99
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 1759
95 % 3 22 2309 Flexibility: Low
Max RMSD: 1.4, Avg RMSD: 1.0
PDBFlex
90 % 3 22 2376
70 % 64 156 153
50 % 92 299 88
40 % 92 299 110
30 % 92 299 121
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 1350
95 % 4 27 1806 Flexibility: Low
Max RMSD: 2.6, Avg RMSD: 1.4
PDBFlex
90 % 4 27 1842
70 % 4 27 1868
50 % 135 355 62
40 % 135 358 74
30 % 135 359 85
Entity #5 | Chains: C
50S ribosomal protein L4 protein, length: 205 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 4 29 1253
95 % 4 29 1666
90 % 4 29 1704
70 % 4 29 1725
50 % 97 185 137
40 % 131 352 77
30 % 131 352 88
Entity #6 | Chains: D
50S ribosomal protein L5 protein, length: 180 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name Structural variation in cluster
100 % 4 24 1592
95 % 4 24 2109 Flexibility: Low
Max RMSD: 2.3, Avg RMSD: 1.4
PDBFlex
90 % 4 24 2159
70 % 97 180 100
50 % 134 351 61
40 % 134 351 81
30 % 134 351 91
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 41307
95 % 1 2 31453 Flexibility: Low
Max RMSD: 0.7, Avg RMSD: 0.7
PDBFlex
90 % 1 2 30103
70 % 1 2 26905
50 % 1 2 22960
40 % 1 2 20207
30 % 1 2 17113
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 15769
95 % 1 5 14764 Flexibility: No
Max RMSD: 0.6, Avg RMSD: 0.5
PDBFlex
90 % 1 5 14491
70 % 1 5 13608
50 % 80 131 183
40 % 106 271 112
30 % 106 279 122
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 2113
95 % 4 21 2367 Flexibility: Low
Max RMSD: 3.8, Avg RMSD: 2.2
PDBFlex
90 % 4 21 2434
70 % 19 62 538
50 % 48 229 146
40 % 48 232 155
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.

You can also use the structure comparison tool to compare any 2 given structures