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 3299
95 % 3 19 3606 Flexibility: Low
Max RMSD: 1.9, Avg RMSD: 1.2
PDBFlex
90 % 3 19 3671
70 % 3 19 3621
50 % 3 19 3424
40 % 3 19 3299
30 % 3 19 3119
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 1972
95 % 4 24 2278 Flexibility: Low
Max RMSD: 1.6, Avg RMSD: 0.8
PDBFlex
90 % 4 24 2336
70 % 113 241 83
50 % 141 415 38
40 % 237 621 23
30 % 237 621 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 1966
95 % 4 24 2272 Flexibility: Low
Max RMSD: 8.4, Avg RMSD: 2.9
PDBFlex
90 % 4 24 2329
70 % 4 24 2330
50 % 140 397 52
40 % 140 397 70
30 % 140 397 87
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 1695
95 % 4 27 2002 Flexibility: Low
Max RMSD: 5.2, Avg RMSD: 2.7
PDBFlex
90 % 4 27 2046
70 % 107 205 96
50 % 140 403 45
40 % 140 403 66
30 % 140 403 79
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 1991
95 % 4 24 2305 Flexibility: Low
Max RMSD: 1.7, Avg RMSD: 0.9
PDBFlex
90 % 4 24 2364
70 % 4 24 2384
50 % 141 399 41
40 % 141 399 58
30 % 141 401 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 2149
95 % 4 24 2304 Flexibility: Low
Max RMSD: 2.8, Avg RMSD: 1.6
PDBFlex
90 % 4 24 2363
70 % 4 24 2362
50 % 140 398 50
40 % 140 398 69
30 % 140 398 86
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 3279
95 % 3 19 3576 Flexibility: Medium
Max RMSD: 7.0, Avg RMSD: 3.0
PDBFlex
90 % 3 19 3639
70 % 3 19 3590
50 % 3 19 3493
40 % 3 19 3355
30 % 3 19 3097
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 1632
95 % 4 28 1915 Flexibility: Low
Max RMSD: 1.4, Avg RMSD: 0.8
PDBFlex
90 % 4 28 1959
70 % 4 28 1983
50 % 141 402 42
40 % 141 410 55
30 % 141 410 70
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 1661
95 % 4 28 1948 Flexibility: Medium
Max RMSD: 7.9, Avg RMSD: 3.7
PDBFlex
90 % 4 28 1989
70 % 4 28 2017
50 % 112 226 119
40 % 140 397 71
30 % 140 397 88
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 1660
95 % 4 30 1805 Flexibility: Low
Max RMSD: 2.5, Avg RMSD: 1.1
PDBFlex
90 % 4 30 1847
70 % 4 30 1863
50 % 4 30 1898
40 % 4 30 1879
30 % 4 30 1822
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 1725
95 % 4 26 2037 Flexibility: Low
Max RMSD: 2.0, Avg RMSD: 1.1
PDBFlex
90 % 4 26 2082
70 % 4 26 2101
50 % 112 235 114
40 % 207 482 42
30 % 207 482 59
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 1845
95 % 4 25 2177 Flexibility: Low
Max RMSD: 3.3, Avg RMSD: 1.6
PDBFlex
90 % 4 25 2233
70 % 4 25 2249
50 % 140 400 48
40 % 140 402 67
30 % 140 402 80
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 2257
95 % 3 25 2557 Flexibility: Low
Max RMSD: 6.5, Avg RMSD: 1.7
PDBFlex
90 % 3 25 2627
70 % 3 25 2621
50 % 3 25 2609
40 % 3 25 2567
30 % 3 25 2392
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 1561
95 % 4 29 1836 Flexibility: Medium
Max RMSD: 11.9, Avg RMSD: 5.0
PDBFlex
90 % 4 29 1879
70 % 33 193 171
50 % 142 400 46
40 % 142 400 68
30 % 142 400 81
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 1724
95 % 4 26 2036 Flexibility: Low
Max RMSD: 2.8, Avg RMSD: 1.5
PDBFlex
90 % 4 26 2081
70 % 4 26 2100
50 % 4 26 2123
40 % 4 26 2096
30 % 207 464 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 1874
95 % 4 24 2191 Flexibility: Low
Max RMSD: 1.8, Avg RMSD: 0.9
PDBFlex
90 % 4 24 2247
70 % 4 24 2263
50 % 37 217 196
40 % 141 403 61
30 % 141 403 74
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 3917
95 % 1 12 4294 Flexibility: No
Max RMSD: 0.5, Avg RMSD: 0.4
PDBFlex
90 % 1 12 4340
70 % 1 12 4255
50 % 103 243 122
40 % 103 260 136
30 % 103 261 150
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 1313
95 % 4 34 1542 Flexibility: Low
Max RMSD: 1.5, Avg RMSD: 0.9
PDBFlex
90 % 4 34 1565
70 % 4 34 1591
50 % 140 388 64
40 % 140 394 78
30 % 140 394 93
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 12968
95 % 1 6 13554 Flexibility: Low
Max RMSD: 0.5, Avg RMSD: 0.5
PDBFlex
90 % 1 6 11782
70 % 1 6 11147
50 % 1 6 9994
40 % 1 6 9038
30 % 1 6 7792
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 1657
95 % 4 28 1942 Flexibility: Low
Max RMSD: 1.8, Avg RMSD: 1.1
PDBFlex
90 % 4 28 1985
70 % 32 189 176
50 % 37 219 193
40 % 37 219 204
30 % 37 219 223
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 1917
95 % 4 24 2223 Flexibility: Low
Max RMSD: 7.5, Avg RMSD: 2.2
PDBFlex
90 % 4 24 2280
70 % 108 202 98
50 % 141 404 43
40 % 141 404 64
30 % 141 404 77
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 1658
95 % 4 28 1943 Flexibility: Low
Max RMSD: 3.7, Avg RMSD: 1.7
PDBFlex
90 % 4 28 1986
70 % 4 28 2013
50 % 108 206 128
40 % 141 392 80
30 % 141 392 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 2195
95 % 3 22 2497 Flexibility: Low
Max RMSD: 1.5, Avg RMSD: 1.0
PDBFlex
90 % 3 22 2563
70 % 100 338 50
50 % 100 341 88
40 % 100 341 105
30 % 100 341 118
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 1676
95 % 4 27 1995 Flexibility: Low
Max RMSD: 2.7, Avg RMSD: 1.5
PDBFlex
90 % 4 27 2038
70 % 4 27 2066
50 % 146 407 47
40 % 146 411 59
30 % 146 412 72
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 1572
95 % 4 29 1850 Flexibility: Low
Max RMSD: 2.2, Avg RMSD: 1.2
PDBFlex
90 % 4 29 1891
70 % 4 29 1908
50 % 108 207 127
40 % 142 404 63
30 % 142 404 76
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 1955
95 % 4 24 2262 Flexibility: Low
Max RMSD: 2.3, Avg RMSD: 1.4
PDBFlex
90 % 4 24 2319
70 % 110 204 94
50 % 147 402 44
40 % 147 402 65
30 % 147 402 78
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 45859
95 % 1 2 38240 Flexibility: Low
Max RMSD: 0.7, Avg RMSD: 0.7
PDBFlex
90 % 1 2 36470
70 % 1 2 32345
50 % 1 2 27501
40 % 1 2 24118
30 % 1 2 20115
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 16855
95 % 1 5 15633 Flexibility: No
Max RMSD: 0.6, Avg RMSD: 0.4
PDBFlex
90 % 1 5 15299
70 % 1 5 14275
50 % 91 152 176
40 % 117 318 106
30 % 117 321 117
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 2222
95 % 4 21 2531 Flexibility: Low
Max RMSD: 3.8, Avg RMSD: 2.1
PDBFlex
90 % 4 21 2600
70 % 20 65 556
50 % 49 251 152
40 % 49 254 161
30 % 49 257 178

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