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 2715
95 % 3 19 3359 Flexibility: Low
Max RMSD: 1.9, Avg RMSD: 1.3
PDBFlex
90 % 3 19 3408
70 % 3 19 3372
50 % 3 19 3285
40 % 3 19 3191
30 % 3 19 2993
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 1618
95 % 4 24 2138 Flexibility: Low
Max RMSD: 1.3, Avg RMSD: 0.8
PDBFlex
90 % 4 24 2191
70 % 102 212 92
50 % 130 363 51
40 % 225 556 20
30 % 225 556 35
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 1613
95 % 4 24 2128 Flexibility: Low
Max RMSD: 3.4, Avg RMSD: 1.9
PDBFlex
90 % 4 24 2179
70 % 4 24 2178
50 % 129 346 65
40 % 129 346 85
30 % 224 533 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 1363
95 % 4 27 1825 Flexibility: Low
Max RMSD: 5.2, Avg RMSD: 2.7
PDBFlex
90 % 4 27 1862
70 % 96 183 101
50 % 129 354 57
40 % 129 354 74
30 % 129 354 85
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 1628
95 % 4 24 2147 Flexibility: Low
Max RMSD: 1.7, Avg RMSD: 0.9
PDBFlex
90 % 4 24 2201
70 % 4 24 2198
50 % 125 326 68
40 % 130 351 69
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 1766
95 % 4 24 2148 Flexibility: Low
Max RMSD: 2.8, Avg RMSD: 1.5
PDBFlex
90 % 4 24 2202
70 % 4 24 2199
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 2719
95 % 3 19 3362 Flexibility: Medium
Max RMSD: 6.7, Avg RMSD: 3.3
PDBFlex
90 % 3 19 3411
70 % 3 19 3377
50 % 3 19 3289
40 % 3 19 3193
30 % 3 19 2996
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 1329
95 % 4 28 1774 Flexibility: Low
Max RMSD: 1.4, Avg RMSD: 0.8
PDBFlex
90 % 4 28 1815
70 % 4 28 1839
50 % 130 351 58
40 % 130 358 66
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 1334
95 % 4 28 1780 Flexibility: Medium
Max RMSD: 7.9, Avg RMSD: 3.5
PDBFlex
90 % 4 28 1820
70 % 4 28 1844
50 % 101 202 125
40 % 129 346 86
30 % 129 346 98
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 1325
95 % 4 30 1643
90 % 4 30 1682
70 % 4 30 1699
50 % 4 30 1737
40 % 4 30 1743
30 % 4 30 1704
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 1459
95 % 4 26 1945
90 % 4 26 1992
70 % 4 26 2019
50 % 96 182 141
40 % 129 352 77
30 % 196 430 62
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 1503
95 % 4 25 2015 Flexibility: Low
Max RMSD: 3.3, Avg RMSD: 1.6
PDBFlex
90 % 4 25 2064
70 % 4 25 2080
50 % 129 349 63
40 % 129 351 80
30 % 129 351 90
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 1806
95 % 3 25 2356 Flexibility: Low
Max RMSD: 6.5, Avg RMSD: 1.8
PDBFlex
90 % 3 25 2422
70 % 3 25 2421
50 % 3 25 2406
40 % 3 25 2388
30 % 3 25 2281
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 1266
95 % 4 29 1687 Flexibility: Medium
Max RMSD: 11.9, Avg RMSD: 5.1
PDBFlex
90 % 4 29 1727
70 % 33 172 172
50 % 131 350 59
40 % 131 350 78
30 % 131 350 88
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 1464
95 % 4 26 1950 Flexibility: Low
Max RMSD: 2.8, Avg RMSD: 1.5
PDBFlex
90 % 4 26 1997
70 % 4 26 2025
50 % 4 26 2033
40 % 4 26 2026
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 1643
95 % 4 24 2168 Flexibility: Low
Max RMSD: 1.8, Avg RMSD: 0.9
PDBFlex
90 % 4 24 2220
70 % 4 24 2212
50 % 37 188 193
40 % 130 352 75
30 % 130 352 87
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 3539
95 % 1 12 4326 Flexibility: No
Max RMSD: 0.5, Avg RMSD: 0.4
PDBFlex
90 % 1 12 4357
70 % 1 12 4279
50 % 92 208 137
40 % 92 219 148
30 % 92 219 159
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 1066
95 % 4 34 1446
90 % 4 34 1472
70 % 4 34 1468
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 14265
95 % 1 6 13511 Flexibility: Low
Max RMSD: 0.5, Avg RMSD: 0.5
PDBFlex
90 % 1 6 13293
70 % 1 6 12503
50 % 1 6 11150
40 % 1 6 10110
30 % 1 6 8816
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 1341
95 % 4 28 1786 Flexibility: Low
Max RMSD: 1.6, Avg RMSD: 1.0
PDBFlex
90 % 4 28 1826
70 % 32 167 174
50 % 37 190 192
40 % 37 190 206
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 1729
95 % 4 24 2090 Flexibility: Low
Max RMSD: 7.5, Avg RMSD: 2.3
PDBFlex
90 % 4 24 2140
70 % 97 180 102
50 % 130 351 61
40 % 130 351 81
30 % 130 351 91
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 1340
95 % 4 28 1785 Flexibility: Low
Max RMSD: 3.7, Avg RMSD: 1.7
PDBFlex
90 % 4 28 1824
70 % 4 28 1849
50 % 97 184 140
40 % 130 344 87
30 % 130 344 100
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 1772
95 % 3 22 2323 Flexibility: Low
Max RMSD: 1.4, Avg RMSD: 1.0
PDBFlex
90 % 3 22 2391
70 % 64 156 154
50 % 92 299 88
40 % 92 299 110
30 % 92 299 122
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 1357
95 % 4 27 1813 Flexibility: Low
Max RMSD: 2.6, Avg RMSD: 1.4
PDBFlex
90 % 4 27 1851
70 % 4 27 1877
50 % 135 355 62
40 % 135 358 76
30 % 135 359 86
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 1258
95 % 4 29 1674
90 % 4 29 1715
70 % 4 29 1738
50 % 97 185 139
40 % 131 352 79
30 % 131 352 89
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 1606
95 % 4 24 2122 Flexibility: Low
Max RMSD: 2.3, Avg RMSD: 1.4
PDBFlex
90 % 4 24 2174
70 % 99 182 100
50 % 136 353 56
40 % 136 353 73
30 % 136 353 84
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 41582
95 % 1 2 31638 Flexibility: Low
Max RMSD: 0.7, Avg RMSD: 0.7
PDBFlex
90 % 1 2 30283
70 % 1 2 27066
50 % 1 2 23100
40 % 1 2 20330
30 % 1 2 17218
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 15902
95 % 1 5 14859 Flexibility: No
Max RMSD: 0.6, Avg RMSD: 0.5
PDBFlex
90 % 1 5 14585
70 % 1 5 13695
50 % 80 131 184
40 % 106 271 112
30 % 106 279 123
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 2129
95 % 4 21 2380 Flexibility: Low
Max RMSD: 3.8, Avg RMSD: 2.2
PDBFlex
90 % 4 21 2448
70 % 19 62 543
50 % 48 229 148
40 % 48 232 159
30 % 48 235 167

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


ACTION - (A) Select for download / view details OR (B) Select two chains for comparison
Rank PDB ID Entity ID Chains Description Details Taxonomy EC Number
1 4IOA 3 A 50S ribosomal protein L2 1299
2 4IO9 3 A 50S ribosomal protein L2 1299
3 1NKW 3 A 50S ribosomal protein L2 1299
4 5JVG 3 A 50S ribosomal protein L2 1299
5 4IOC 3 A 50S ribosomal protein L2 1299
6 5JVH 3 A 50S ribosomal protein L2 1299
7 2ZJR 3 A 50S ribosomal protein L2 1299
8 3PIO 3 A 50S ribosomal protein L2 1299
9 4WFN 1 A 50S ribosomal protein L2 1299
10 4U67 1 A 50S ribosomal protein L2 1299
11 3PIP 3 A 50S ribosomal protein L2 1299
12 3CF5 6 A 50S RIBOSOMAL PROTEIN L2 1299
13 3DLL 3 A 50S ribosomal protein L2 1299
14 1NWY 3 A ribosomal protein L2 1299
15 1SM1 8 A 50S RIBOSOMAL PROTEIN L2 1299
16 2ZJQ 3 A 50S ribosomal protein L2 1299
17 1NWX 3 A ribosomal protein L2 1299
18 1XBP 3 A 50S ribosomal protein L2 1299
19 2ZJP 6 A 50S RIBOSOMAL PROTEIN L2 1299
20 4V49 25 BA 50S ribosomal protein L2 562
21 4V4A 23 BA 50S ribosomal protein L2 562
22 4V4G 24 BD, DD, FD, HD, JD 50S ribosomal protein L2 562