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 2594
95 % 3 19 3232 Flexibility: Low
Max RMSD: 1.9, Avg RMSD: 1.2
PDBFlex
90 % 3 19 3279
70 % 3 19 3246
50 % 3 19 3174
40 % 3 19 3092
30 % 3 19 2900
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 1557
95 % 4 24 2067 Flexibility: Low
Max RMSD: 1.6, Avg RMSD: 0.8
PDBFlex
90 % 4 24 2121
70 % 100 204 84
50 % 128 352 53
40 % 221 534 20
30 % 221 534 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 1553
95 % 4 24 2055 Flexibility: Low
Max RMSD: 8.4, Avg RMSD: 2.9
PDBFlex
90 % 4 24 2106
70 % 4 24 2106
50 % 4 24 2095
40 % 127 335 82
30 % 220 514 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 1306
95 % 4 27 1764 Flexibility: Low
Max RMSD: 5.2, Avg RMSD: 2.7
PDBFlex
90 % 4 27 1801
70 % 94 181 91
50 % 127 343 56
40 % 127 343 71
30 % 127 343 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 1567
95 % 4 24 2075 Flexibility: Low
Max RMSD: 1.7, Avg RMSD: 0.9
PDBFlex
90 % 4 24 2130
70 % 4 24 2129
50 % 123 321 66
40 % 128 343 67
30 % 128 345 81
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 1697
95 % 4 24 2076 Flexibility: Low
Max RMSD: 2.8, Avg RMSD: 1.6
PDBFlex
90 % 4 24 2131
70 % 4 24 2130
50 % 127 337 63
40 % 127 337 81
30 % 127 337 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 2597
95 % 3 19 3235 Flexibility: Medium
Max RMSD: 7.0, Avg RMSD: 3.2
PDBFlex
90 % 3 19 3282
70 % 3 19 3251
50 % 3 19 3178
40 % 3 19 3094
30 % 3 19 2903
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 1277
95 % 4 28 1724 Flexibility: Low
Max RMSD: 1.4, Avg RMSD: 0.8
PDBFlex
90 % 4 28 1757
70 % 4 28 1777
50 % 128 340 57
40 % 128 347 68
30 % 128 347 82
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 1281
95 % 4 28 1728 Flexibility: Medium
Max RMSD: 7.9, Avg RMSD: 3.8
PDBFlex
90 % 4 28 1761
70 % 4 28 1782
50 % 99 197 121
40 % 127 335 83
30 % 127 335 94
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 1273
95 % 4 30 1591 Flexibility: Low
Max RMSD: 2.5, Avg RMSD: 1.0
PDBFlex
90 % 4 30 1627
70 % 4 30 1640
50 % 4 30 1674
40 % 4 30 1684
30 % 4 30 1650
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 Structural variation in cluster
100 % 4 26 1403
95 % 4 26 1884 Flexibility: Low
Max RMSD: 2.0, Avg RMSD: 1.1
PDBFlex
90 % 4 26 1931
70 % 4 26 1951
50 % 94 180 130
40 % 127 341 75
30 % 194 419 58
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 1448
95 % 4 25 1957 Flexibility: Low
Max RMSD: 3.3, Avg RMSD: 1.6
PDBFlex
90 % 4 25 2006
70 % 4 25 2017
50 % 127 338 62
40 % 127 338 80
30 % 127 340 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 1735
95 % 3 25 2279 Flexibility: Low
Max RMSD: 6.5, Avg RMSD: 1.7
PDBFlex
90 % 3 25 2343
70 % 3 25 2342
50 % 3 25 2326
40 % 3 25 2308
30 % 3 25 2216
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 1217
95 % 4 29 1635 Flexibility: Medium
Max RMSD: 11.9, Avg RMSD: 4.9
PDBFlex
90 % 4 29 1669
70 % 33 169 168
50 % 129 339 58
40 % 129 339 76
30 % 129 339 87
Entity #24 | Chains: W
50S ribosomal protein L29 protein, length: 67 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 4 26 1408
95 % 4 26 1890
90 % 4 26 1936
70 % 4 26 1957
50 % 4 26 1963
40 % 4 26 1957
30 % 194 409 65
Entity #25 | Chains: X
50S ribosomal protein L30 protein, length: 55 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 4 24 1580
95 % 4 24 2096
90 % 4 24 2149
70 % 4 24 2144
50 % 37 181 187
40 % 128 341 72
30 % 128 341 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 3401
95 % 1 12 4172 Flexibility: No
Max RMSD: 0.5, Avg RMSD: 0.4
PDBFlex
90 % 1 12 4202
70 % 1 12 4128
50 % 90 203 126
40 % 90 207 143
30 % 90 210 156
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 1025
95 % 4 34 1406 Flexibility: Low
Max RMSD: 1.5, Avg RMSD: 0.9
PDBFlex
90 % 4 34 1427
70 % 4 34 1425
50 % 99 197 123
40 % 127 334 87
30 % 127 334 98
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 13759
95 % 1 6 13058 Flexibility: Low
Max RMSD: 0.5, Avg RMSD: 0.5
PDBFlex
90 % 1 6 12848
70 % 1 6 12056
50 % 1 6 10763
40 % 1 6 9767
30 % 1 6 8504
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 1287
95 % 4 28 1733 Flexibility: Low
Max RMSD: 1.8, Avg RMSD: 1.1
PDBFlex
90 % 4 28 1768
70 % 32 163 169
50 % 37 181 188
40 % 37 181 206
30 % 37 181 215
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 1662
95 % 4 24 2020 Flexibility: Low
Max RMSD: 7.5, Avg RMSD: 2.2
PDBFlex
90 % 4 24 2069
70 % 95 178 93
50 % 128 340 59
40 % 128 340 78
30 % 128 340 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 1286
95 % 4 28 1732 Flexibility: Low
Max RMSD: 3.7, Avg RMSD: 1.8
PDBFlex
90 % 4 28 1766
70 % 4 28 1788
50 % 95 182 129
40 % 128 333 86
30 % 128 333 97
Entity #31 | Chains: 4
50S ribosomal protein L36 protein, length: 36 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 3 22 1707
95 % 3 22 2248
90 % 3 22 2314
70 % 63 149 152
50 % 91 289 87
40 % 91 289 108
30 % 91 289 120
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 1301
95 % 4 27 1757 Flexibility: Low
Max RMSD: 2.7, Avg RMSD: 1.6
PDBFlex
90 % 4 27 1794
70 % 4 27 1818
50 % 133 344 61
40 % 133 347 73
30 % 133 348 85
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 1207
95 % 4 29 1621 Flexibility: Low
Max RMSD: 2.2, Avg RMSD: 1.2
PDBFlex
90 % 4 29 1657
70 % 4 29 1678
50 % 95 183 127
40 % 129 341 77
30 % 129 341 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 1545
95 % 4 24 2050 Flexibility: Low
Max RMSD: 2.3, Avg RMSD: 1.4
PDBFlex
90 % 4 24 2101
70 % 95 178 92
50 % 132 340 60
40 % 132 340 79
30 % 132 340 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 40151
95 % 1 2 30559 Flexibility: Low
Max RMSD: 0.7, Avg RMSD: 0.7
PDBFlex
90 % 1 2 29277
70 % 1 2 26275
50 % 1 2 22464
40 % 1 2 19771
30 % 1 2 16743
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 15310
95 % 1 5 14348 Flexibility: No
Max RMSD: 0.6, Avg RMSD: 0.4
PDBFlex
90 % 1 5 14074
70 % 1 5 13204
50 % 78 129 183
40 % 104 268 109
30 % 104 273 119
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 2038
95 % 4 21 2302 Flexibility: Low
Max RMSD: 3.8, Avg RMSD: 2.1
PDBFlex
90 % 4 21 2367
70 % 19 62 491
50 % 48 229 135
40 % 48 232 149
30 % 48 235 163

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.