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 2786
95 % 3 19 3445 Flexibility: Low
Max RMSD: 1.9, Avg RMSD: 1.3
PDBFlex
90 % 3 19 3504
70 % 3 19 3462
50 % 3 19 3382
40 % 3 19 3278
30 % 3 19 3077
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 1659
95 % 4 24 2209 Flexibility: Low
Max RMSD: 1.3, Avg RMSD: 0.8
PDBFlex
90 % 4 24 2265
70 % 110 225 84
50 % 138 382 42
40 % 234 583 20
30 % 234 583 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 1655
95 % 4 24 2201 Flexibility: Low
Max RMSD: 3.4, Avg RMSD: 1.9
PDBFlex
90 % 4 24 2255
70 % 4 24 2252
50 % 137 364 61
40 % 137 364 81
30 % 233 558 40
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 1413
95 % 4 27 1902 Flexibility: Low
Max RMSD: 5.2, Avg RMSD: 2.7
PDBFlex
90 % 4 27 1945
70 % 104 196 97
50 % 137 374 44
40 % 137 374 62
30 % 137 374 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 1668
95 % 4 24 2217 Flexibility: Low
Max RMSD: 1.7, Avg RMSD: 0.9
PDBFlex
90 % 4 24 2274
70 % 4 24 2271
50 % 133 344 64
40 % 138 370 59
30 % 138 372 76
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 1827
95 % 4 24 2218 Flexibility: Low
Max RMSD: 2.8, Avg RMSD: 1.5
PDBFlex
90 % 4 24 2275
70 % 4 24 2272
50 % 137 367 58
40 % 137 367 77
30 % 137 367 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 2790
95 % 3 19 3448 Flexibility: Medium
Max RMSD: 6.7, Avg RMSD: 3.3
PDBFlex
90 % 3 19 3507
70 % 3 19 3467
50 % 3 19 3386
40 % 3 19 3280
30 % 3 19 3080
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 1376
95 % 4 28 1852 Flexibility: Low
Max RMSD: 1.4, Avg RMSD: 0.8
PDBFlex
90 % 4 28 1891
70 % 4 28 1908
50 % 138 369 48
40 % 138 377 58
30 % 138 377 75
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 1381
95 % 4 28 1857 Flexibility: Medium
Max RMSD: 7.9, Avg RMSD: 3.5
PDBFlex
90 % 4 28 1895
70 % 4 28 1914
50 % 109 215 118
40 % 137 364 82
30 % 137 364 95
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 1371
95 % 4 30 1707
90 % 4 30 1748
70 % 4 30 1758
50 % 4 30 1790
40 % 4 30 1791
30 % 4 30 1751
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 1503
95 % 4 26 2030
90 % 4 26 2078
70 % 4 26 2087
50 % 104 195 133
40 % 137 370 71
30 % 204 449 65
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 1541
95 % 4 25 2082 Flexibility: Low
Max RMSD: 3.3, Avg RMSD: 1.6
PDBFlex
90 % 4 25 2134
70 % 4 25 2144
50 % 137 367 59
40 % 137 369 76
30 % 137 369 91
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 1867
95 % 3 25 2435 Flexibility: Low
Max RMSD: 6.5, Avg RMSD: 1.8
PDBFlex
90 % 3 25 2499
70 % 3 25 2505
50 % 3 25 2485
40 % 3 25 2452
30 % 3 25 2341
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 1310
95 % 4 29 1768 Flexibility: Medium
Max RMSD: 11.9, Avg RMSD: 5.1
PDBFlex
90 % 4 29 1809
70 % 33 178 173
50 % 139 369 52
40 % 139 369 69
30 % 139 369 86
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 1508
95 % 4 26 2037 Flexibility: Low
Max RMSD: 2.8, Avg RMSD: 1.5
PDBFlex
90 % 4 26 2085
70 % 4 26 2094
50 % 4 26 2096
40 % 4 26 2090
30 % 204 435 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 1685
95 % 4 24 2237 Flexibility: Low
Max RMSD: 1.8, Avg RMSD: 0.9
PDBFlex
90 % 4 24 2293
70 % 4 24 2286
50 % 37 193 196
40 % 138 370 70
30 % 138 370 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 3641
95 % 1 12 4440 Flexibility: No
Max RMSD: 0.5, Avg RMSD: 0.4
PDBFlex
90 % 1 12 4480
70 % 1 12 4388
50 % 100 226 125
40 % 100 237 140
30 % 100 238 145
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 1102
95 % 4 34 1484
90 % 4 34 1508
70 % 4 34 1508
50 % 109 215 121
40 % 137 366 78
30 % 137 366 94
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 14665
95 % 1 6 13871 Flexibility: Low
Max RMSD: 0.5, Avg RMSD: 0.5
PDBFlex
90 % 1 6 13640
70 % 1 6 12804
50 % 1 6 11413
40 % 1 6 10339
30 % 1 6 9009
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 1389
95 % 4 28 1863 Flexibility: Low
Max RMSD: 1.6, Avg RMSD: 1.0
PDBFlex
90 % 4 28 1902
70 % 32 172 175
50 % 37 195 191
40 % 37 195 206
30 % 37 195 216
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 1786
95 % 4 24 2158 Flexibility: Low
Max RMSD: 7.5, Avg RMSD: 2.3
PDBFlex
90 % 4 24 2210
70 % 105 193 99
50 % 138 373 46
40 % 234 560 22
30 % 234 560 39
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 1388
95 % 4 28 1862 Flexibility: Low
Max RMSD: 3.7, Avg RMSD: 1.7
PDBFlex
90 % 4 28 1900
70 % 4 28 1920
50 % 105 197 130
40 % 138 362 84
30 % 138 362 96
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 1835
95 % 3 22 2403 Flexibility: Low
Max RMSD: 1.4, Avg RMSD: 1.0
PDBFlex
90 % 3 22 2469
70 % 72 170 148
50 % 100 318 87
40 % 100 318 105
30 % 100 318 119
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 1407
95 % 4 27 1892 Flexibility: Low
Max RMSD: 2.6, Avg RMSD: 1.4
PDBFlex
90 % 4 27 1933
70 % 4 27 1950
50 % 143 374 57
40 % 143 378 63
30 % 143 379 79
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 1295
95 % 4 29 1750
90 % 4 29 1793
70 % 4 29 1802
50 % 105 198 127
40 % 139 370 74
30 % 139 371 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 1648
95 % 4 24 2194 Flexibility: Low
Max RMSD: 2.3, Avg RMSD: 1.4
PDBFlex
90 % 4 24 2247
70 % 107 195 95
50 % 144 371 47
40 % 144 371 64
30 % 144 371 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 42566
95 % 1 2 32335 Flexibility: Low
Max RMSD: 0.7, Avg RMSD: 0.7
PDBFlex
90 % 1 2 30932
70 % 1 2 27620
50 % 1 2 23536
40 % 1 2 20714
30 % 1 2 17535
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 16353
95 % 1 5 15238 Flexibility: No
Max RMSD: 0.6, Avg RMSD: 0.5
PDBFlex
90 % 1 5 14954
70 % 1 5 14018
50 % 88 144 178
40 % 114 289 110
30 % 114 297 120
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 2196
95 % 4 21 2461 Flexibility: Low
Max RMSD: 3.8, Avg RMSD: 2.2
PDBFlex
90 % 4 21 2524
70 % 20 63 548
50 % 49 235 149
40 % 49 238 159
30 % 49 241 168

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 13 K 50S ribosomal protein L17 1299
2 4IO9 13 K 50S ribosomal protein L17 1299
3 5DM6 12 K 50S ribosomal protein L17 1299
4 1NKW 14 L 50S ribosomal protein L17 1299
5 5JVG 13 K 50S ribosomal protein L17 1299
6 4IOC 13 K 50S ribosomal protein L17 1299
7 5JVH 12 K 50S ribosomal protein L17 1299
8 2ZJR 13 K 50S ribosomal protein L17 1299
9 3PIO 13 K 50S ribosomal protein L17 1299
10 5DM7 12 K 50S ribosomal protein L17 1299
11 4WFN 10 K 50S ribosomal protein L17 1299
12 4U67 10 K 50S ribosomal protein L17 1299
13 3PIP 13 K 50S ribosomal protein L17 1299
14 3CF5 16 K 50S RIBOSOMAL PROTEIN L17 1299
15 3DLL 13 K 50S ribosomal protein L17 1299
16 1NWY 14 L ribosomal protein L17 1299
17 1SM1 19 L 50S RIBOSOMAL PROTEIN L17 1299
18 2ZJQ 13 K 50S ribosomal protein L17 1299
19 1NWX 14 L ribosomal protein L17 1299
20 1XBP 14 L 50S ribosomal protein L17 1299
21 2ZJP 16 K 50S RIBOSOMAL PROTEIN L17 1299
22 4V49 36 BL 50S ribosomal protein L17 562
23 4V4A 34 BL 50S ribosomal protein L17 562
24 4V4G 35 BO, DO, FO, HO, JO 50S ribosomal protein L17 562