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 3244
95 % 3 19 3545 Flexibility: Low
Max RMSD: 1.9, Avg RMSD: 1.2
PDBFlex
90 % 3 19 3616
70 % 3 19 3562
50 % 3 19 3378
40 % 3 19 3255
30 % 3 19 3087
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 1946
95 % 4 24 2252 Flexibility: Low
Max RMSD: 1.6, Avg RMSD: 0.8
PDBFlex
90 % 4 24 2306
70 % 113 232 84
50 % 141 403 39
40 % 237 609 22
30 % 237 609 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 1893
95 % 4 24 2200 Flexibility: Low
Max RMSD: 8.4, Avg RMSD: 2.9
PDBFlex
90 % 4 24 2254
70 % 4 24 2267
50 % 140 385 54
40 % 140 385 74
30 % 140 385 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 1678
95 % 4 27 1979 Flexibility: Low
Max RMSD: 5.2, Avg RMSD: 2.7
PDBFlex
90 % 4 27 2018
70 % 107 203 96
50 % 140 391 48
40 % 140 391 68
30 % 140 391 83
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 1965
95 % 4 24 2279 Flexibility: Low
Max RMSD: 1.7, Avg RMSD: 0.9
PDBFlex
90 % 4 24 2334
70 % 4 24 2357
50 % 141 384 45
40 % 141 391 57
30 % 141 393 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 2122
95 % 4 24 2278 Flexibility: Low
Max RMSD: 2.8, Avg RMSD: 1.6
PDBFlex
90 % 4 24 2333
70 % 4 24 2334
50 % 140 386 52
40 % 140 386 73
30 % 140 386 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 3223
95 % 3 19 3519 Flexibility: Medium
Max RMSD: 7.0, Avg RMSD: 3.0
PDBFlex
90 % 3 19 3585
70 % 3 19 3529
50 % 3 19 3443
40 % 3 19 3303
30 % 3 19 3065
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 1609
95 % 4 28 1884 Flexibility: Low
Max RMSD: 1.4, Avg RMSD: 0.8
PDBFlex
90 % 4 28 1925
70 % 4 28 1944
50 % 141 390 42
40 % 141 398 56
30 % 141 398 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 1634
95 % 4 28 1916 Flexibility: Medium
Max RMSD: 7.9, Avg RMSD: 3.7
PDBFlex
90 % 4 28 1954
70 % 4 28 1975
50 % 112 222 119
40 % 140 385 75
30 % 140 385 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 1633
95 % 4 30 1783 Flexibility: Low
Max RMSD: 2.5, Avg RMSD: 1.1
PDBFlex
90 % 4 30 1820
70 % 4 30 1831
50 % 4 30 1863
40 % 4 30 1842
30 % 4 30 1788
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 1703
95 % 4 26 2009 Flexibility: Low
Max RMSD: 2.0, Avg RMSD: 1.1
PDBFlex
90 % 4 26 2048
70 % 4 26 2059
50 % 107 202 130
40 % 207 470 45
30 % 207 470 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 1818
95 % 4 25 2150 Flexibility: Low
Max RMSD: 3.3, Avg RMSD: 1.6
PDBFlex
90 % 4 25 2200
70 % 4 25 2214
50 % 140 388 51
40 % 140 390 70
30 % 140 390 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 2219
95 % 3 25 2520 Flexibility: Low
Max RMSD: 6.5, Avg RMSD: 1.7
PDBFlex
90 % 3 25 2596
70 % 3 25 2587
50 % 3 25 2569
40 % 3 25 2525
30 % 3 25 2360
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 1538
95 % 4 29 1810 Flexibility: Medium
Max RMSD: 11.9, Avg RMSD: 5.0
PDBFlex
90 % 4 29 1848
70 % 33 190 173
50 % 142 388 49
40 % 142 388 71
30 % 142 388 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 1702
95 % 4 26 1990 Flexibility: Low
Max RMSD: 2.8, Avg RMSD: 1.5
PDBFlex
90 % 4 26 2029
70 % 4 26 2042
50 % 4 26 2088
40 % 4 26 2058
30 % 207 456 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 1848
95 % 4 24 2163 Flexibility: Low
Max RMSD: 1.8, Avg RMSD: 0.9
PDBFlex
90 % 4 24 2213
70 % 4 24 2227
50 % 37 207 194
40 % 141 391 63
30 % 141 391 78
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 3842
95 % 1 12 4213 Flexibility: No
Max RMSD: 0.5, Avg RMSD: 0.4
PDBFlex
90 % 1 12 4263
70 % 1 12 4183
50 % 103 237 122
40 % 103 248 141
30 % 103 249 149
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 1287
95 % 4 34 1518 Flexibility: Low
Max RMSD: 1.5, Avg RMSD: 0.9
PDBFlex
90 % 4 34 1535
70 % 4 34 1558
50 % 140 381 65
40 % 140 387 72
30 % 140 387 88
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 12730
95 % 1 6 13315 Flexibility: Low
Max RMSD: 0.5, Avg RMSD: 0.5
PDBFlex
90 % 1 6 11581
70 % 1 6 10950
50 % 1 6 9847
40 % 1 6 8916
30 % 1 6 7687
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 1630
95 % 4 28 1910 Flexibility: Low
Max RMSD: 1.8, Avg RMSD: 1.1
PDBFlex
90 % 4 28 1950
70 % 32 186 176
50 % 37 209 193
40 % 37 209 209
30 % 37 209 227
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 1897
95 % 4 24 2203 Flexibility: Low
Max RMSD: 7.5, Avg RMSD: 2.2
PDBFlex
90 % 4 24 2256
70 % 108 200 98
50 % 141 392 46
40 % 141 392 66
30 % 141 392 81
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 1631
95 % 4 28 1911 Flexibility: Low
Max RMSD: 3.7, Avg RMSD: 1.7
PDBFlex
90 % 4 28 1951
70 % 4 28 1971
50 % 108 204 127
40 % 141 380 83
30 % 141 380 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 2159
95 % 3 22 2426 Flexibility: Low
Max RMSD: 1.5, Avg RMSD: 1.0
PDBFlex
90 % 3 22 2537
70 % 100 326 50
50 % 100 329 88
40 % 100 329 107
30 % 100 329 120
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 1655
95 % 4 27 1973 Flexibility: Low
Max RMSD: 2.7, Avg RMSD: 1.5
PDBFlex
90 % 4 27 2012
70 % 4 27 2030
50 % 146 395 50
40 % 146 399 60
30 % 146 400 75
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 1550
95 % 4 29 1822 Flexibility: Low
Max RMSD: 2.2, Avg RMSD: 1.2
PDBFlex
90 % 4 29 1859
70 % 4 29 1874
50 % 108 205 126
40 % 142 392 65
30 % 142 392 80
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 1931
95 % 4 24 2237 Flexibility: Low
Max RMSD: 2.3, Avg RMSD: 1.4
PDBFlex
90 % 4 24 2290
70 % 110 202 95
50 % 147 390 47
40 % 147 390 67
30 % 147 390 82
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 45179
95 % 1 2 37675 Flexibility: Low
Max RMSD: 0.7, Avg RMSD: 0.7
PDBFlex
90 % 1 2 35946
70 % 1 2 31907
50 % 1 2 27123
40 % 1 2 23778
30 % 1 2 19814
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 16521
95 % 1 5 15319 Flexibility: No
Max RMSD: 0.6, Avg RMSD: 0.4
PDBFlex
90 % 1 5 15002
70 % 1 5 14031
50 % 91 150 177
40 % 117 308 106
30 % 117 311 118
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 2186
95 % 4 21 2553 Flexibility: Low
Max RMSD: 3.8, Avg RMSD: 2.1
PDBFlex
90 % 4 21 2571
70 % 20 65 555
50 % 49 245 151
40 % 49 248 163
30 % 49 251 175

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 28 2 50S ribosomal protein L34 1299
2 4IO9 28 2 50S ribosomal protein L34 1299
3 5DM6 27 2 50S ribosomal protein L34 1299
4 1NKW 29 2 50S ribosomal protein L34 1299
5 5JVG 28 2 50S ribosomal protein L34 1299
6 4IOC 28 2 50S ribosomal protein L34 1299
7 5JVH 27 2 50S ribosomal protein L34 1299
8 2ZJR 28 2 50S ribosomal protein L34 1299
9 3PIO 28 2 50S ribosomal protein L34 1299
10 5DM7 27 2 50S ribosomal protein L34 1299
11 4WFN 25 2 50S ribosomal protein L34 1299
12 4U67 25 2 50S ribosomal protein L34 1299
13 3PIP 28 2 50S ribosomal protein L34 1299
14 3CF5 2 2 50S RIBOSOMAL PROTEIN L34 1299
15 3DLL 28 2 50S ribosomal protein L34 1299
16 1NWY 29 2 ribosomal protein L34 1299
17 1SM1 3 2 50S RIBOSOMAL PROTEIN L34 1299
18 2ZJQ 28 2 50S ribosomal protein L34 1299
19 1NWX 29 2 ribosomal protein L34 1299
20 1XBP 29 2 50S ribosomal protein L34 1299
21 2ZJP 2 2 50S RIBOSOMAL PROTEIN L34 1299
22 4V4P 31 A7 50S ribosomal protein L34 274
23 4V4R 53 B7 50S ribosomal protein L34 274
24 4V4S 53 B7 50S ribosomal protein L34 274
25 4V4T 52 B7 50S ribosomal protein L34 274
26 4V49 52 B2 50S ribosomal protein L34 562
27 4V4A 50 B2 50S ribosomal protein L34 562
28 4V4G 50 B4, D4, F4, H4, J4 50S ribosomal protein L34 562