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 3287
95 % 3 19 3590 Flexibility: Low
Max RMSD: 1.9, Avg RMSD: 1.2
PDBFlex
90 % 3 19 3657
70 % 3 19 3606
50 % 3 19 3415
40 % 3 19 3289
30 % 3 19 3111
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 1966
95 % 4 24 2268 Flexibility: Low
Max RMSD: 1.6, Avg RMSD: 0.8
PDBFlex
90 % 4 24 2323
70 % 113 234 83
50 % 141 408 40
40 % 237 614 23
30 % 237 614 39
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 1906
95 % 4 24 2211 Flexibility: Low
Max RMSD: 8.4, Avg RMSD: 2.9
PDBFlex
90 % 4 24 2266
70 % 4 24 2282
50 % 140 390 62
40 % 140 390 80
30 % 140 390 93
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 1690
95 % 4 27 1996 Flexibility: Low
Max RMSD: 5.2, Avg RMSD: 2.7
PDBFlex
90 % 4 27 2038
70 % 107 203 96
50 % 140 396 51
40 % 140 396 72
30 % 140 396 86
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 1986
95 % 4 24 2296 Flexibility: Low
Max RMSD: 1.7, Avg RMSD: 0.9
PDBFlex
90 % 4 24 2352
70 % 4 24 2374
50 % 141 389 46
40 % 141 396 58
30 % 141 398 71
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 2141
95 % 4 24 2295 Flexibility: Low
Max RMSD: 2.8, Avg RMSD: 1.6
PDBFlex
90 % 4 24 2351
70 % 4 24 2353
50 % 140 391 61
40 % 140 391 78
30 % 140 391 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 3266
95 % 3 19 3563 Flexibility: Medium
Max RMSD: 7.0, Avg RMSD: 3.0
PDBFlex
90 % 3 19 3627
70 % 3 19 3576
50 % 3 19 3485
40 % 3 19 3346
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 1627
95 % 4 28 1908 Flexibility: Low
Max RMSD: 1.4, Avg RMSD: 0.8
PDBFlex
90 % 4 28 1950
70 % 4 28 1974
50 % 141 395 43
40 % 141 403 57
30 % 141 403 73
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 1655
95 % 4 28 1941 Flexibility: Medium
Max RMSD: 7.9, Avg RMSD: 3.7
PDBFlex
90 % 4 28 1980
70 % 4 28 2006
50 % 112 224 119
40 % 140 390 81
30 % 140 390 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 1654
95 % 4 30 1801 Flexibility: Low
Max RMSD: 2.5, Avg RMSD: 1.1
PDBFlex
90 % 4 30 1840
70 % 4 30 1854
50 % 4 30 1888
40 % 4 30 1866
30 % 4 30 1810
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 2028 Flexibility: Low
Max RMSD: 2.0, Avg RMSD: 1.1
PDBFlex
90 % 4 26 2071
70 % 4 26 2090
50 % 107 202 130
40 % 207 475 45
30 % 207 475 64
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 1838
95 % 4 25 2169 Flexibility: Low
Max RMSD: 3.3, Avg RMSD: 1.6
PDBFlex
90 % 4 25 2222
70 % 4 25 2238
50 % 140 393 57
40 % 140 395 73
30 % 140 395 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 2245
95 % 3 25 2546 Flexibility: Low
Max RMSD: 6.5, Avg RMSD: 1.7
PDBFlex
90 % 3 25 2618
70 % 3 25 2610
50 % 3 25 2598
40 % 3 25 2553
30 % 3 25 2381
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 1556
95 % 4 29 1831 Flexibility: Medium
Max RMSD: 11.9, Avg RMSD: 5.0
PDBFlex
90 % 4 29 1871
70 % 33 193 169
50 % 142 393 55
40 % 142 393 74
30 % 142 393 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 1719
95 % 4 26 2027 Flexibility: Low
Max RMSD: 2.8, Avg RMSD: 1.5
PDBFlex
90 % 4 26 2070
70 % 4 26 2089
50 % 4 26 2113
40 % 4 26 2082
30 % 207 461 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 1867
95 % 4 24 2183 Flexibility: Low
Max RMSD: 1.8, Avg RMSD: 0.9
PDBFlex
90 % 4 24 2236
70 % 4 24 2251
50 % 37 212 194
40 % 141 396 65
30 % 141 396 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 3894
95 % 1 12 4270 Flexibility: No
Max RMSD: 0.5, Avg RMSD: 0.4
PDBFlex
90 % 1 12 4320
70 % 1 12 4235
50 % 103 241 121
40 % 103 253 136
30 % 103 254 146
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 1306
95 % 4 34 1535 Flexibility: Low
Max RMSD: 1.5, Avg RMSD: 0.9
PDBFlex
90 % 4 34 1555
70 % 4 34 1582
50 % 140 386 64
40 % 140 392 77
30 % 140 392 91
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 12853
95 % 1 6 13440 Flexibility: Low
Max RMSD: 0.5, Avg RMSD: 0.5
PDBFlex
90 % 1 6 11674
70 % 1 6 11051
50 % 1 6 9933
40 % 1 6 8989
30 % 1 6 7756
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 1651
95 % 4 28 1935 Flexibility: Low
Max RMSD: 1.8, Avg RMSD: 1.1
PDBFlex
90 % 4 28 1976
70 % 32 189 174
50 % 37 214 193
40 % 37 214 206
30 % 37 214 225
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 2214 Flexibility: Low
Max RMSD: 7.5, Avg RMSD: 2.2
PDBFlex
90 % 4 24 2268
70 % 108 200 98
50 % 141 397 49
40 % 141 397 69
30 % 141 397 83
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 1652
95 % 4 28 1936 Flexibility: Low
Max RMSD: 3.7, Avg RMSD: 1.7
PDBFlex
90 % 4 28 1977
70 % 4 28 2002
50 % 108 204 127
40 % 141 385 82
30 % 141 385 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 2184
95 % 3 22 2441 Flexibility: Low
Max RMSD: 1.5, Avg RMSD: 1.0
PDBFlex
90 % 3 22 2554
70 % 100 331 48
50 % 100 334 88
40 % 100 334 106
30 % 100 334 119
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 1670
95 % 4 27 1989 Flexibility: Low
Max RMSD: 2.7, Avg RMSD: 1.5
PDBFlex
90 % 4 27 2031
70 % 4 27 2055
50 % 146 400 56
40 % 146 404 60
30 % 146 405 76
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 1568
95 % 4 29 1844 Flexibility: Low
Max RMSD: 2.2, Avg RMSD: 1.2
PDBFlex
90 % 4 29 1883
70 % 4 29 1900
50 % 108 205 126
40 % 142 397 67
30 % 142 397 82
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 2253 Flexibility: Low
Max RMSD: 2.3, Avg RMSD: 1.4
PDBFlex
90 % 4 24 2307
70 % 110 202 95
50 % 147 395 50
40 % 147 395 71
30 % 147 395 85
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 45538
95 % 1 2 37958 Flexibility: Low
Max RMSD: 0.7, Avg RMSD: 0.7
PDBFlex
90 % 1 2 36195
70 % 1 2 32099
50 % 1 2 27290
40 % 1 2 23923
30 % 1 2 19943
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 16723
95 % 1 5 15507 Flexibility: No
Max RMSD: 0.6, Avg RMSD: 0.4
PDBFlex
90 % 1 5 15183
70 % 1 5 14190
50 % 91 150 178
40 % 117 311 107
30 % 117 314 118
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 2211
95 % 4 21 2520 Flexibility: Low
Max RMSD: 3.8, Avg RMSD: 2.1
PDBFlex
90 % 4 21 2591
70 % 20 65 556
50 % 49 246 151
40 % 49 249 164
30 % 49 252 175

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 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