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 3410
95 % 3 19 3713 Flexibility: Low
Max RMSD: 1.9, Avg RMSD: 1.2
PDBFlex
90 % 3 19 3771
70 % 3 19 3708
50 % 3 19 3496
40 % 3 19 3360
30 % 3 19 3162
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 2050
95 % 4 24 2349 Flexibility: Low
Max RMSD: 1.6, Avg RMSD: 0.8
PDBFlex
90 % 4 24 2415
70 % 113 251 84
50 % 142 428 38
40 % 238 647 23
30 % 238 647 40
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 2044
95 % 4 24 2343 Flexibility: Low
Max RMSD: 8.4, Avg RMSD: 2.9
PDBFlex
90 % 4 24 2408
70 % 4 24 2399
50 % 141 410 50
40 % 141 410 71
30 % 141 410 86
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 1758
95 % 4 27 2063 Flexibility: Low
Max RMSD: 5.2, Avg RMSD: 2.7
PDBFlex
90 % 4 27 2115
70 % 107 214 96
50 % 141 416 45
40 % 141 416 64
30 % 141 416 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 2069
95 % 4 24 2375 Flexibility: Low
Max RMSD: 1.7, Avg RMSD: 0.9
PDBFlex
90 % 4 24 2440
70 % 4 24 2453
50 % 142 412 40
40 % 142 412 56
30 % 142 414 74
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 2224
95 % 4 24 2374 Flexibility: Low
Max RMSD: 2.8, Avg RMSD: 1.6
PDBFlex
90 % 4 24 2439
70 % 4 24 2431
50 % 141 411 49
40 % 141 411 70
30 % 141 411 85
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 3384
95 % 3 19 3682 Flexibility: Medium
Max RMSD: 7.0, Avg RMSD: 3.0
PDBFlex
90 % 3 19 3741
70 % 3 19 3681
50 % 3 19 3560
40 % 3 19 3411
30 % 3 19 3144
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 1688
95 % 4 28 1969 Flexibility: Low
Max RMSD: 1.4, Avg RMSD: 0.8
PDBFlex
90 % 4 28 2016
70 % 4 28 2040
50 % 142 415 42
40 % 142 423 53
30 % 142 423 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 1715
95 % 4 28 2003 Flexibility: Medium
Max RMSD: 7.9, Avg RMSD: 3.7
PDBFlex
90 % 4 28 2052
70 % 4 28 2079
50 % 112 236 117
40 % 141 410 72
30 % 141 410 87
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 1681
95 % 4 30 1817 Flexibility: Low
Max RMSD: 2.5, Avg RMSD: 1.1
PDBFlex
90 % 4 30 1857
70 % 4 30 1881
50 % 4 30 1901
40 % 4 30 1889
30 % 4 30 1829
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 1795
95 % 4 26 2094 Flexibility: Low
Max RMSD: 2.0, Avg RMSD: 1.1
PDBFlex
90 % 4 26 2149
70 % 4 26 2164
50 % 112 245 114
40 % 208 496 40
30 % 208 496 60
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 1919
95 % 4 25 2249 Flexibility: Low
Max RMSD: 3.3, Avg RMSD: 1.6
PDBFlex
90 % 4 25 2308
70 % 4 25 2314
50 % 141 413 48
40 % 141 415 65
30 % 141 415 81
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 2328
95 % 3 25 2628 Flexibility: Low
Max RMSD: 6.5, Avg RMSD: 1.7
PDBFlex
90 % 3 25 2699
70 % 3 25 2692
50 % 3 25 2669
40 % 3 25 2621
30 % 3 25 2437
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 1617
95 % 4 29 1890 Flexibility: Medium
Max RMSD: 11.9, Avg RMSD: 5.0
PDBFlex
90 % 4 29 1938
70 % 34 196 168
50 % 143 413 46
40 % 143 413 66
30 % 143 413 82
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 1794
95 % 4 26 2093 Flexibility: Low
Max RMSD: 2.8, Avg RMSD: 1.5
PDBFlex
90 % 4 26 2148
70 % 4 26 2163
50 % 4 26 2174
40 % 4 26 2140
30 % 208 477 65
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 1953
95 % 4 24 2263 Flexibility: Low
Max RMSD: 1.8, Avg RMSD: 0.9
PDBFlex
90 % 4 24 2323
70 % 4 24 2329
50 % 38 221 197
40 % 142 416 60
30 % 142 416 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 4053
95 % 1 12 4422 Flexibility: No
Max RMSD: 0.5, Avg RMSD: 0.4
PDBFlex
90 % 1 12 4461
70 % 1 12 4363
50 % 103 253 120
40 % 104 271 135
30 % 104 272 146
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 1370
95 % 4 34 1606 Flexibility: Low
Max RMSD: 1.5, Avg RMSD: 0.9
PDBFlex
90 % 4 34 1629
70 % 4 34 1646
50 % 141 401 60
40 % 141 407 73
30 % 141 407 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 13273
95 % 1 6 13878 Flexibility: Low
Max RMSD: 0.5, Avg RMSD: 0.5
PDBFlex
90 % 1 6 12481
70 % 1 6 11775
50 % 1 6 10180
40 % 1 6 9197
30 % 1 6 7930
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 1712
95 % 4 28 1997 Flexibility: Low
Max RMSD: 1.8, Avg RMSD: 1.1
PDBFlex
90 % 4 28 2048
70 % 33 192 175
50 % 38 223 196
40 % 38 223 206
30 % 38 223 226
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 1993
95 % 4 24 2293 Flexibility: Low
Max RMSD: 7.5, Avg RMSD: 2.2
PDBFlex
90 % 4 24 2355
70 % 108 211 98
50 % 142 417 43
40 % 142 417 62
30 % 142 417 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 1713
95 % 4 28 1998 Flexibility: Low
Max RMSD: 3.7, Avg RMSD: 1.7
PDBFlex
90 % 4 28 2049
70 % 4 28 2073
50 % 108 215 130
40 % 142 405 78
30 % 142 405 90
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 2268
95 % 3 22 2565 Flexibility: Low
Max RMSD: 1.5, Avg RMSD: 1.0
PDBFlex
90 % 3 22 2634
70 % 100 350 50
50 % 100 353 86
40 % 100 353 101
30 % 100 353 116
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 1734
95 % 4 27 2056 Flexibility: Low
Max RMSD: 2.7, Avg RMSD: 1.5
PDBFlex
90 % 4 27 2108
70 % 4 27 2132
50 % 148 421 47
40 % 148 425 58
30 % 148 426 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 1631
95 % 4 29 1907 Flexibility: Low
Max RMSD: 2.2, Avg RMSD: 1.2
PDBFlex
90 % 4 29 1952
70 % 4 29 1973
50 % 108 216 129
40 % 143 417 61
30 % 143 417 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 2088
95 % 4 24 2357 Flexibility: Low
Max RMSD: 2.3, Avg RMSD: 1.4
PDBFlex
90 % 4 24 2422
70 % 110 213 94
50 % 148 415 44
40 % 148 415 63
30 % 148 415 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 46787
95 % 1 2 38968 Flexibility: Low
Max RMSD: 0.7, Avg RMSD: 0.7
PDBFlex
90 % 1 2 37142
70 % 1 2 32900
50 % 1 2 27995
40 % 1 2 24546
30 % 1 2 20459
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 17245
95 % 1 5 15993 Flexibility: No
Max RMSD: 0.6, Avg RMSD: 0.4
PDBFlex
90 % 1 5 15641
70 % 1 5 14565
50 % 91 158 174
40 % 118 326 103
30 % 118 329 117
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 2297
95 % 4 21 2601 Flexibility: Low
Max RMSD: 3.8, Avg RMSD: 2.1
PDBFlex
90 % 4 21 2671
70 % 20 65 574
50 % 50 254 157
40 % 50 257 164
30 % 50 260 182

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