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 3289
95 % 3 19 3595 Flexibility: Low
Max RMSD: 1.9, Avg RMSD: 1.2
PDBFlex
90 % 3 19 3660
70 % 3 19 3608
50 % 3 19 3413
40 % 3 19 3290
30 % 3 19 3112
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 1967
95 % 4 24 2270 Flexibility: Low
Max RMSD: 1.6, Avg RMSD: 0.8
PDBFlex
90 % 4 24 2327
70 % 113 240 82
50 % 141 414 39
40 % 237 620 23
30 % 237 620 38
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 1961
95 % 4 24 2264 Flexibility: Low
Max RMSD: 8.4, Avg RMSD: 2.9
PDBFlex
90 % 4 24 2320
70 % 4 24 2322
50 % 140 396 55
40 % 140 396 73
30 % 140 396 90
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 1692
95 % 4 27 1997 Flexibility: Low
Max RMSD: 5.2, Avg RMSD: 2.7
PDBFlex
90 % 4 27 2041
70 % 107 205 95
50 % 140 402 45
40 % 140 402 66
30 % 140 402 80
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 1987
95 % 4 24 2298 Flexibility: Low
Max RMSD: 1.7, Avg RMSD: 0.9
PDBFlex
90 % 4 24 2356
70 % 4 24 2376
50 % 141 399 41
40 % 141 399 57
30 % 141 401 72
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 2144
95 % 4 24 2297 Flexibility: Low
Max RMSD: 2.8, Avg RMSD: 1.6
PDBFlex
90 % 4 24 2355
70 % 4 24 2355
50 % 140 397 51
40 % 140 397 69
30 % 140 397 86
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 3267
95 % 3 19 3566 Flexibility: Medium
Max RMSD: 7.0, Avg RMSD: 3.0
PDBFlex
90 % 3 19 3628
70 % 3 19 3577
50 % 3 19 3482
40 % 3 19 3347
30 % 3 19 3091
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 1629
95 % 4 28 1910 Flexibility: Low
Max RMSD: 1.4, Avg RMSD: 0.8
PDBFlex
90 % 4 28 1953
70 % 4 28 1978
50 % 141 401 42
40 % 141 409 55
30 % 141 409 71
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 1657
95 % 4 28 1943 Flexibility: Medium
Max RMSD: 7.9, Avg RMSD: 3.7
PDBFlex
90 % 4 28 1983
70 % 4 28 2010
50 % 112 226 119
40 % 140 396 74
30 % 140 396 91
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 1656
95 % 4 30 1802 Flexibility: Low
Max RMSD: 2.5, Avg RMSD: 1.1
PDBFlex
90 % 4 30 1842
70 % 4 30 1857
50 % 4 30 1891
40 % 4 30 1869
30 % 4 30 1813
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 1720
95 % 4 26 2029 Flexibility: Low
Max RMSD: 2.0, Avg RMSD: 1.1
PDBFlex
90 % 4 26 2074
70 % 4 26 2093
50 % 112 234 113
40 % 207 481 42
30 % 207 481 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 1839
95 % 4 25 2171 Flexibility: Low
Max RMSD: 3.3, Avg RMSD: 1.6
PDBFlex
90 % 4 25 2226
70 % 4 25 2240
50 % 140 399 48
40 % 140 401 67
30 % 140 401 82
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 2248
95 % 3 25 2550 Flexibility: Low
Max RMSD: 6.5, Avg RMSD: 1.7
PDBFlex
90 % 3 25 2620
70 % 3 25 2612
50 % 3 25 2599
40 % 3 25 2555
30 % 3 25 2383
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 1557
95 % 4 29 1832 Flexibility: Medium
Max RMSD: 11.9, Avg RMSD: 5.0
PDBFlex
90 % 4 29 1873
70 % 33 193 169
50 % 142 399 46
40 % 142 399 68
30 % 142 399 83
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 1719
95 % 4 26 2028 Flexibility: Low
Max RMSD: 2.8, Avg RMSD: 1.5
PDBFlex
90 % 4 26 2073
70 % 4 26 2092
50 % 4 26 2116
40 % 4 26 2085
30 % 207 464 66
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 1868
95 % 4 24 2184 Flexibility: Low
Max RMSD: 1.8, Avg RMSD: 0.9
PDBFlex
90 % 4 24 2239
70 % 4 24 2254
50 % 37 216 194
40 % 141 402 62
30 % 141 402 76
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 3901
95 % 1 12 4279 Flexibility: No
Max RMSD: 0.5, Avg RMSD: 0.4
PDBFlex
90 % 1 12 4326
70 % 1 12 4242
50 % 103 243 121
40 % 103 259 134
30 % 103 260 147
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 1307
95 % 4 34 1538 Flexibility: Low
Max RMSD: 1.5, Avg RMSD: 0.9
PDBFlex
90 % 4 34 1557
70 % 4 34 1582
50 % 140 388 63
40 % 140 394 78
30 % 140 394 93
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 12924
95 % 1 6 13508 Flexibility: Low
Max RMSD: 0.5, Avg RMSD: 0.5
PDBFlex
90 % 1 6 11738
70 % 1 6 11109
50 % 1 6 9966
40 % 1 6 9015
30 % 1 6 7774
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 1653
95 % 4 28 1937 Flexibility: Low
Max RMSD: 1.8, Avg RMSD: 1.1
PDBFlex
90 % 4 28 1979
70 % 32 189 174
50 % 37 218 191
40 % 37 218 202
30 % 37 218 222
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 % 4 24 1910
95 % 4 24 2215 Flexibility: Low
Max RMSD: 7.5, Avg RMSD: 2.2
PDBFlex
90 % 4 24 2271
70 % 108 202 97
50 % 141 403 43
40 % 141 403 64
30 % 141 403 78
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 1654
95 % 4 28 1938 Flexibility: Low
Max RMSD: 3.7, Avg RMSD: 1.7
PDBFlex
90 % 4 28 1980
70 % 4 28 2006
50 % 108 206 127
40 % 141 391 81
30 % 141 391 95
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 2186
95 % 3 22 2490 Flexibility: Low
Max RMSD: 1.5, Avg RMSD: 1.0
PDBFlex
90 % 3 22 2556
70 % 100 337 49
50 % 100 340 86
40 % 100 340 104
30 % 100 340 117
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 1672
95 % 4 27 1990 Flexibility: Low
Max RMSD: 2.7, Avg RMSD: 1.5
PDBFlex
90 % 4 27 2034
70 % 4 27 2059
50 % 146 406 47
40 % 146 410 60
30 % 146 411 73
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 1569
95 % 4 29 1845 Flexibility: Low
Max RMSD: 2.2, Avg RMSD: 1.2
PDBFlex
90 % 4 29 1885
70 % 4 29 1903
50 % 108 207 126
40 % 142 403 63
30 % 142 403 77
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 1950
95 % 4 24 2254 Flexibility: Low
Max RMSD: 2.3, Avg RMSD: 1.4
PDBFlex
90 % 4 24 2310
70 % 110 204 92
50 % 147 401 44
40 % 147 401 65
30 % 147 401 79
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 45674
95 % 1 2 38078 Flexibility: Low
Max RMSD: 0.7, Avg RMSD: 0.7
PDBFlex
90 % 1 2 36317
70 % 1 2 32193
50 % 1 2 27367
40 % 1 2 23995
30 % 1 2 20010
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 16796
95 % 1 5 15579 Flexibility: No
Max RMSD: 0.6, Avg RMSD: 0.4
PDBFlex
90 % 1 5 15251
70 % 1 5 14235
50 % 91 152 175
40 % 117 317 105
30 % 117 320 116
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 % 4 21 2214
95 % 4 21 2524 Flexibility: Low
Max RMSD: 3.8, Avg RMSD: 2.1
PDBFlex
90 % 4 21 2593
70 % 20 65 555
50 % 49 250 151
40 % 49 253 161
30 % 49 256 175

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 5DM6 2 A 50S ribosomal protein L2 1299
4 1NKW 3 A 50S ribosomal protein L2 1299
5 5JVG 3 A 50S ribosomal protein L2 1299
6 4IOC 3 A 50S ribosomal protein L2 1299
7 5JVH 3 A 50S ribosomal protein L2 1299
8 2ZJR 3 A 50S ribosomal protein L2 1299
9 3PIO 3 A 50S ribosomal protein L2 1299
10 5DM7 2 A 50S ribosomal protein L2 1299
11 4WFN 1 A 50S ribosomal protein L2 1299
12 4U67 1 A 50S ribosomal protein L2 1299
13 3PIP 3 A 50S ribosomal protein L2 1299
14 3CF5 6 A 50S RIBOSOMAL PROTEIN L2 1299
15 3DLL 3 A 50S ribosomal protein L2 1299
16 1NWY 3 A ribosomal protein L2 1299
17 1SM1 8 A 50S RIBOSOMAL PROTEIN L2 1299
18 2ZJQ 3 A 50S ribosomal protein L2 1299
19 1NWX 3 A ribosomal protein L2 1299
20 1XBP 3 A 50S ribosomal protein L2 1299
21 2ZJP 6 A 50S RIBOSOMAL PROTEIN L2 1299
22 4V49 25 BA 50S ribosomal protein L2 562
23 4V4A 23 BA 50S ribosomal protein L2 562
24 4V4G 24 BD, DD, FD, HD, JD 50S ribosomal protein L2 562