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 3383
95 % 3 19 3685 Flexibility: Low
Max RMSD: 1.9, Avg RMSD: 1.2
PDBFlex
90 % 3 19 3740
70 % 3 19 3681
50 % 3 19 3480
40 % 3 19 3346
30 % 3 19 3155
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 2030
95 % 4 24 2333 Flexibility: Low
Max RMSD: 1.6, Avg RMSD: 0.8
PDBFlex
90 % 4 24 2398
70 % 113 251 83
50 % 142 427 38
40 % 238 644 23
30 % 238 644 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 2024
95 % 4 24 2327 Flexibility: Low
Max RMSD: 8.4, Avg RMSD: 2.9
PDBFlex
90 % 4 24 2391
70 % 4 24 2378
50 % 141 409 50
40 % 141 409 71
30 % 141 409 84
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 1736
95 % 4 27 2048 Flexibility: Low
Max RMSD: 5.2, Avg RMSD: 2.7
PDBFlex
90 % 4 27 2099
70 % 107 214 95
50 % 141 415 44
40 % 141 415 63
30 % 141 415 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 2050
95 % 4 24 2360 Flexibility: Low
Max RMSD: 1.7, Avg RMSD: 0.9
PDBFlex
90 % 4 24 2424
70 % 4 24 2434
50 % 142 411 39
40 % 142 411 55
30 % 142 413 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 2206
95 % 4 24 2359 Flexibility: Low
Max RMSD: 2.8, Avg RMSD: 1.6
PDBFlex
90 % 4 24 2423
70 % 4 24 2411
50 % 141 410 48
40 % 141 410 69
30 % 141 410 83
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 3359
95 % 3 19 3653 Flexibility: Medium
Max RMSD: 7.0, Avg RMSD: 3.0
PDBFlex
90 % 3 19 3709
70 % 3 19 3653
50 % 3 19 3545
40 % 3 19 3397
30 % 3 19 3135
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 1669
95 % 4 28 1954 Flexibility: Low
Max RMSD: 1.4, Avg RMSD: 0.8
PDBFlex
90 % 4 28 2001
70 % 4 28 2021
50 % 142 414 41
40 % 142 422 53
30 % 142 422 71
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 1697
95 % 4 28 1987 Flexibility: Medium
Max RMSD: 7.9, Avg RMSD: 3.7
PDBFlex
90 % 4 28 2035
70 % 4 28 2057
50 % 112 236 115
40 % 141 409 72
30 % 141 409 85
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 1696
95 % 4 30 1839 Flexibility: Low
Max RMSD: 2.5, Avg RMSD: 1.1
PDBFlex
90 % 4 30 1882
70 % 4 30 1900
50 % 4 30 1926
40 % 4 30 1906
30 % 4 30 1849
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 1773
95 % 4 26 2081 Flexibility: Low
Max RMSD: 2.0, Avg RMSD: 1.1
PDBFlex
90 % 4 26 2135
70 % 4 26 2143
50 % 112 245 112
40 % 208 495 39
30 % 208 495 58
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 1897
95 % 4 25 2230 Flexibility: Low
Max RMSD: 3.3, Avg RMSD: 1.6
PDBFlex
90 % 4 25 2291
70 % 4 25 2293
50 % 141 412 47
40 % 141 414 65
30 % 141 414 79
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 2307
95 % 3 25 2609 Flexibility: Low
Max RMSD: 6.5, Avg RMSD: 1.7
PDBFlex
90 % 3 25 2678
70 % 3 25 2670
50 % 3 25 2647
40 % 3 25 2603
30 % 3 25 2431
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 1602
95 % 4 29 1875 Flexibility: Medium
Max RMSD: 11.9, Avg RMSD: 5.0
PDBFlex
90 % 4 29 1922
70 % 34 195 167
50 % 143 412 45
40 % 143 412 66
30 % 143 412 80
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 1772
95 % 4 26 2080 Flexibility: Low
Max RMSD: 2.8, Avg RMSD: 1.5
PDBFlex
90 % 4 26 2134
70 % 4 26 2142
50 % 4 26 2160
40 % 4 26 2126
30 % 208 476 63
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 1932
95 % 4 24 2244 Flexibility: Low
Max RMSD: 1.8, Avg RMSD: 0.9
PDBFlex
90 % 4 24 2305
70 % 4 24 2308
50 % 38 220 195
40 % 142 415 58
30 % 142 415 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 4029
95 % 1 12 4397 Flexibility: No
Max RMSD: 0.5, Avg RMSD: 0.4
PDBFlex
90 % 1 12 4438
70 % 1 12 4336
50 % 103 252 118
40 % 104 270 132
30 % 104 271 145
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 1359
95 % 4 34 1599 Flexibility: Low
Max RMSD: 1.5, Avg RMSD: 0.9
PDBFlex
90 % 4 34 1622
70 % 4 34 1634
50 % 141 400 60
40 % 141 406 74
30 % 141 406 86
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 13189
95 % 1 6 13790 Flexibility: Low
Max RMSD: 0.5, Avg RMSD: 0.5
PDBFlex
90 % 1 6 12405
70 % 1 6 11708
50 % 1 6 10136
40 % 1 6 9160
30 % 1 6 7897
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 1693
95 % 4 28 1981 Flexibility: Low
Max RMSD: 1.8, Avg RMSD: 1.1
PDBFlex
90 % 4 28 2031
70 % 33 191 173
50 % 38 222 193
40 % 38 222 203
30 % 38 222 223
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 1973
95 % 4 24 2274 Flexibility: Low
Max RMSD: 7.5, Avg RMSD: 2.2
PDBFlex
90 % 4 24 2336
70 % 108 211 97
50 % 142 416 42
40 % 142 416 61
30 % 142 416 76
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 1694
95 % 4 28 1982 Flexibility: Low
Max RMSD: 3.7, Avg RMSD: 1.7
PDBFlex
90 % 4 28 2032
70 % 4 28 2053
50 % 108 215 129
40 % 142 404 78
30 % 142 404 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 2248
95 % 3 22 2550 Flexibility: Low
Max RMSD: 1.5, Avg RMSD: 1.0
PDBFlex
90 % 3 22 2617
70 % 100 349 49
50 % 100 352 86
40 % 100 352 101
30 % 100 352 116
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 1714
95 % 4 27 2041 Flexibility: Low
Max RMSD: 2.7, Avg RMSD: 1.5
PDBFlex
90 % 4 27 2091
70 % 4 27 2109
50 % 148 420 46
40 % 148 424 57
30 % 148 425 73
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 1616
95 % 4 29 1891 Flexibility: Low
Max RMSD: 2.2, Avg RMSD: 1.2
PDBFlex
90 % 4 29 1935
70 % 4 29 1950
50 % 108 216 128
40 % 143 416 59
30 % 143 416 75
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 2011
95 % 4 24 2317 Flexibility: Low
Max RMSD: 2.3, Avg RMSD: 1.4
PDBFlex
90 % 4 24 2380
70 % 110 213 93
50 % 148 414 43
40 % 148 414 62
30 % 148 414 77
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 46497
95 % 1 2 38754 Flexibility: Low
Max RMSD: 0.7, Avg RMSD: 0.7
PDBFlex
90 % 1 2 36934
70 % 1 2 32720
50 % 1 2 27846
40 % 1 2 24423
30 % 1 2 20375
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 17130
95 % 1 5 15884 Flexibility: No
Max RMSD: 0.6, Avg RMSD: 0.4
PDBFlex
90 % 1 5 15541
70 % 1 5 14472
50 % 91 158 172
40 % 118 325 103
30 % 118 328 117
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 2275
95 % 4 21 2584 Flexibility: Low
Max RMSD: 3.8, Avg RMSD: 2.1
PDBFlex
90 % 4 21 2652
70 % 20 65 566
50 % 50 253 155
40 % 50 256 163
30 % 50 259 180

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