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 3179
95 % 3 19 3492 Flexibility: Low
Max RMSD: 1.9, Avg RMSD: 1.2
PDBFlex
90 % 3 19 3562
70 % 3 19 3506
50 % 3 19 3329
40 % 3 19 3214
30 % 3 19 3037
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 1912
95 % 4 24 2213 Flexibility: Low
Max RMSD: 1.6, Avg RMSD: 0.8
PDBFlex
90 % 4 24 2270
70 % 111 228 85
50 % 139 392 42
40 % 235 595 21
30 % 235 595 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 1854
95 % 4 24 2157 Flexibility: Low
Max RMSD: 8.4, Avg RMSD: 2.9
PDBFlex
90 % 4 24 2211
70 % 4 24 2223
50 % 138 374 54
40 % 138 374 75
30 % 138 374 91
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 1637
95 % 4 27 1943 Flexibility: Low
Max RMSD: 5.2, Avg RMSD: 2.7
PDBFlex
90 % 4 27 1985
70 % 105 199 98
50 % 138 382 45
40 % 138 382 63
30 % 138 382 78
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 1932
95 % 4 24 2237 Flexibility: Low
Max RMSD: 1.7, Avg RMSD: 0.9
PDBFlex
90 % 4 24 2295
70 % 4 24 2317
50 % 139 373 46
40 % 139 380 58
30 % 139 382 75
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 2087
95 % 4 24 2236 Flexibility: Low
Max RMSD: 2.8, Avg RMSD: 1.6
PDBFlex
90 % 4 24 2294
70 % 4 24 2296
50 % 138 376 53
40 % 138 376 73
30 % 138 376 89
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 3159
95 % 3 19 3468 Flexibility: Medium
Max RMSD: 7.0, Avg RMSD: 3.0
PDBFlex
90 % 3 19 3532
70 % 3 19 3474
50 % 3 19 3394
40 % 3 19 3262
30 % 3 19 3016
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 1577
95 % 4 28 1854 Flexibility: Low
Max RMSD: 1.4, Avg RMSD: 0.8
PDBFlex
90 % 4 28 1894
70 % 4 28 1912
50 % 139 379 44
40 % 139 387 57
30 % 139 387 76
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 1601
95 % 4 28 1883 Flexibility: Medium
Max RMSD: 7.9, Avg RMSD: 3.7
PDBFlex
90 % 4 28 1923
70 % 4 28 1945
50 % 110 218 120
40 % 138 374 76
30 % 138 374 92
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 1600
95 % 4 30 1752 Flexibility: Low
Max RMSD: 2.5, Avg RMSD: 1.1
PDBFlex
90 % 4 30 1791
70 % 4 30 1800
50 % 4 30 1825
40 % 4 30 1813
30 % 4 30 1762
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 1666
95 % 4 26 1972 Flexibility: Low
Max RMSD: 2.0, Avg RMSD: 1.1
PDBFlex
90 % 4 26 2014
70 % 4 26 2024
50 % 105 198 131
40 % 205 459 45
30 % 205 459 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 1783
95 % 4 25 2110 Flexibility: Low
Max RMSD: 3.3, Avg RMSD: 1.6
PDBFlex
90 % 4 25 2162
70 % 4 25 2173
50 % 138 377 52
40 % 138 379 70
30 % 138 379 86
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 2176
95 % 3 25 2479 Flexibility: Low
Max RMSD: 6.5, Avg RMSD: 1.7
PDBFlex
90 % 3 25 2557
70 % 3 25 2546
50 % 3 25 2531
40 % 3 25 2491
30 % 3 25 2331
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 1506
95 % 4 29 1778 Flexibility: Medium
Max RMSD: 11.9, Avg RMSD: 5.0
PDBFlex
90 % 4 29 1821
70 % 33 184 173
50 % 140 378 49
40 % 140 378 68
30 % 140 378 84
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 1665
95 % 4 26 1953 Flexibility: Low
Max RMSD: 2.8, Avg RMSD: 1.5
PDBFlex
90 % 4 26 1996
70 % 4 26 2008
50 % 4 26 2051
40 % 4 26 2026
30 % 205 445 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 1812
95 % 4 24 2124 Flexibility: Low
Max RMSD: 1.8, Avg RMSD: 0.9
PDBFlex
90 % 4 24 2175
70 % 4 24 2187
50 % 37 200 192
40 % 139 380 66
30 % 139 380 81
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 3774
95 % 1 12 4142 Flexibility: No
Max RMSD: 0.5, Avg RMSD: 0.4
PDBFlex
90 % 1 12 4190
70 % 1 12 4117
50 % 101 232 122
40 % 101 243 140
30 % 101 244 150
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 1263
95 % 4 34 1490 Flexibility: Low
Max RMSD: 1.5, Avg RMSD: 0.9
PDBFlex
90 % 4 34 1511
70 % 4 34 1528
50 % 138 370 65
40 % 138 376 74
30 % 138 376 90
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 12567
95 % 1 6 13154 Flexibility: Low
Max RMSD: 0.5, Avg RMSD: 0.5
PDBFlex
90 % 1 6 11447
70 % 1 6 10806
50 % 1 6 9718
40 % 1 6 8801
30 % 1 6 7596
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 1597
95 % 4 28 1877 Flexibility: Low
Max RMSD: 1.8, Avg RMSD: 1.1
PDBFlex
90 % 4 28 1919
70 % 32 179 176
50 % 37 202 190
40 % 37 202 208
30 % 37 202 226
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 1858
95 % 4 24 2160 Flexibility: Low
Max RMSD: 7.5, Avg RMSD: 2.2
PDBFlex
90 % 4 24 2213
70 % 106 196 99
50 % 139 382 47
40 % 139 382 64
30 % 139 382 79
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 1598
95 % 4 28 1878 Flexibility: Low
Max RMSD: 3.7, Avg RMSD: 1.7
PDBFlex
90 % 4 28 1920
70 % 4 28 1940
50 % 106 200 130
40 % 139 371 77
30 % 139 371 94
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 2119
95 % 3 22 2425 Flexibility: Low
Max RMSD: 1.5, Avg RMSD: 1.0
PDBFlex
90 % 3 22 2498
70 % 100 320 49
50 % 100 323 88
40 % 100 323 107
30 % 100 323 121
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 1617
95 % 4 27 1937 Flexibility: Low
Max RMSD: 2.7, Avg RMSD: 1.5
PDBFlex
90 % 4 27 1978
70 % 4 27 1995
50 % 144 384 51
40 % 144 388 62
30 % 144 389 77
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 1518
95 % 4 29 1791 Flexibility: Low
Max RMSD: 2.2, Avg RMSD: 1.2
PDBFlex
90 % 4 29 1831
70 % 4 29 1844
50 % 106 201 129
40 % 140 381 67
30 % 140 381 83
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 1894
95 % 4 24 2197 Flexibility: Low
Max RMSD: 2.3, Avg RMSD: 1.4
PDBFlex
90 % 4 24 2250
70 % 108 198 96
50 % 145 380 48
40 % 145 380 65
30 % 145 380 80
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 44669
95 % 1 2 37287 Flexibility: Low
Max RMSD: 0.7, Avg RMSD: 0.7
PDBFlex
90 % 1 2 35582
70 % 1 2 31605
50 % 1 2 26881
40 % 1 2 23574
30 % 1 2 19643
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 16305
95 % 1 5 15142 Flexibility: No
Max RMSD: 0.6, Avg RMSD: 0.4
PDBFlex
90 % 1 5 14834
70 % 1 5 13876
50 % 89 147 181
40 % 115 300 109
30 % 115 303 122
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 % 4 21 2146
95 % 4 21 2508 Flexibility: Low
Max RMSD: 3.8, Avg RMSD: 2.1
PDBFlex
90 % 4 21 2530
70 % 20 63 555
50 % 49 238 152
40 % 49 241 164
30 % 49 244 176

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 25 W 50S ribosomal protein L30 1299
2 4IO9 25 W 50S ribosomal protein L30 1299
3 5DM6 24 W 50S ribosomal protein L30 1299
4 1NKW 25 X 50S ribosomal protein L30 1299
5 5JVG 25 W 50S ribosomal protein L30 1299
6 4IOC 25 W 50S ribosomal protein L30 1299
7 5JVH 24 W 50S ribosomal protein L30 1299
8 2ZJR 25 W 50S ribosomal protein L30 1299
9 3PIO 25 W 50S ribosomal protein L30 1299
10 5DM7 24 W 50S ribosomal protein L30 1299
11 4WFN 22 W 50S ribosomal protein L30 1299
12 4U67 22 W 50S ribosomal protein L30 1299
13 3PIP 25 W 50S ribosomal protein L30 1299
14 3CF5 28 W 50S RIBOSOMAL PROTEIN L30 1299
15 3DLL 25 W 50S ribosomal protein L30 1299
16 1NWY 25 X ribosomal protein L30 1299
17 1SM1 30 X 50S RIBOSOMAL PROTEIN L30 1299
18 2ZJQ 25 W 50S ribosomal protein L30 1299
19 1NWX 25 X ribosomal protein L30 1299
20 1XBP 25 X 50S ribosomal protein L30 1299
21 2ZJP 28 W 50S RIBOSOMAL PROTEIN L30 1299
22 4V49 48 BX 50S ribosomal protein L30 562
23 4V4A 46 BX 50S ribosomal protein L30 562
24 4V4G 46 BZ, DZ, FZ, HZ, JZ 50S ribosomal protein L30 562