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 3380
95 % 3 19 3682 Flexibility: Low
Max RMSD: 1.9, Avg RMSD: 1.2
PDBFlex
90 % 3 19 3735
70 % 3 19 3677
50 % 3 19 3477
40 % 3 19 3342
30 % 3 19 3145
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 2028
95 % 4 24 2329 Flexibility: Low
Max RMSD: 1.6, Avg RMSD: 0.8
PDBFlex
90 % 4 24 2395
70 % 113 249 84
50 % 142 425 38
40 % 238 642 23
30 % 238 642 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 2023
95 % 4 24 2323 Flexibility: Low
Max RMSD: 8.4, Avg RMSD: 2.9
PDBFlex
90 % 4 24 2388
70 % 4 24 2375
50 % 141 407 56
40 % 141 407 73
30 % 141 407 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 1736
95 % 4 27 2046 Flexibility: Low
Max RMSD: 5.2, Avg RMSD: 2.7
PDBFlex
90 % 4 27 2097
70 % 107 212 96
50 % 141 413 44
40 % 141 413 65
30 % 141 413 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 2048
95 % 4 24 2355 Flexibility: Low
Max RMSD: 1.7, Avg RMSD: 0.9
PDBFlex
90 % 4 24 2421
70 % 4 24 2431
50 % 142 409 40
40 % 142 409 57
30 % 142 411 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 2205
95 % 4 24 2354 Flexibility: Low
Max RMSD: 2.8, Avg RMSD: 1.6
PDBFlex
90 % 4 24 2420
70 % 4 24 2408
50 % 141 408 52
40 % 141 408 71
30 % 141 408 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 3355
95 % 3 19 3650 Flexibility: Medium
Max RMSD: 7.0, Avg RMSD: 3.0
PDBFlex
90 % 3 19 3704
70 % 3 19 3649
50 % 3 19 3543
40 % 3 19 3394
30 % 3 19 3125
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 1953 Flexibility: Low
Max RMSD: 1.4, Avg RMSD: 0.8
PDBFlex
90 % 4 28 2000
70 % 4 28 2020
50 % 142 412 41
40 % 142 420 53
30 % 142 420 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 1697
95 % 4 28 1986 Flexibility: Medium
Max RMSD: 7.9, Avg RMSD: 3.7
PDBFlex
90 % 4 28 2034
70 % 4 28 2056
50 % 112 234 117
40 % 141 407 74
30 % 141 407 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 1696
95 % 4 30 1837 Flexibility: Low
Max RMSD: 2.5, Avg RMSD: 1.1
PDBFlex
90 % 4 30 1880
70 % 4 30 1899
50 % 4 30 1926
40 % 4 30 1906
30 % 4 30 1845
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 1772
95 % 4 26 2080 Flexibility: Low
Max RMSD: 2.0, Avg RMSD: 1.1
PDBFlex
90 % 4 26 2134
70 % 4 26 2139
50 % 112 243 113
40 % 208 493 40
30 % 208 493 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 1897
95 % 4 25 2227 Flexibility: Low
Max RMSD: 3.3, Avg RMSD: 1.6
PDBFlex
90 % 4 25 2288
70 % 4 25 2291
50 % 141 410 48
40 % 141 412 66
30 % 141 412 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 2303
95 % 3 25 2603 Flexibility: Low
Max RMSD: 6.5, Avg RMSD: 1.7
PDBFlex
90 % 3 25 2675
70 % 3 25 2664
50 % 3 25 2644
40 % 3 25 2599
30 % 3 25 2422
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 1601
95 % 4 29 1873 Flexibility: Medium
Max RMSD: 11.9, Avg RMSD: 5.0
PDBFlex
90 % 4 29 1920
70 % 34 195 167
50 % 143 410 45
40 % 143 410 67
30 % 143 410 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 1771
95 % 4 26 2079 Flexibility: Low
Max RMSD: 2.8, Avg RMSD: 1.5
PDBFlex
90 % 4 26 2133
70 % 4 26 2138
50 % 4 26 2157
40 % 4 26 2124
30 % 208 474 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 1932
95 % 4 24 2241 Flexibility: Low
Max RMSD: 1.8, Avg RMSD: 0.9
PDBFlex
90 % 4 24 2302
70 % 4 24 2306
50 % 38 220 195
40 % 142 413 61
30 % 142 413 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 4018
95 % 1 12 4387 Flexibility: No
Max RMSD: 0.5, Avg RMSD: 0.4
PDBFlex
90 % 1 12 4427
70 % 1 12 4328
50 % 103 250 119
40 % 104 268 134
30 % 104 269 147
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 1360
95 % 4 34 1598 Flexibility: Low
Max RMSD: 1.5, Avg RMSD: 0.9
PDBFlex
90 % 4 34 1621
70 % 4 34 1633
50 % 141 398 60
40 % 141 404 79
30 % 141 404 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 13161
95 % 1 6 13749 Flexibility: Low
Max RMSD: 0.5, Avg RMSD: 0.5
PDBFlex
90 % 1 6 12373
70 % 1 6 11684
50 % 1 6 10107
40 % 1 6 9132
30 % 1 6 7868
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 1980 Flexibility: Low
Max RMSD: 1.8, Avg RMSD: 1.1
PDBFlex
90 % 4 28 2030
70 % 33 191 172
50 % 38 222 193
40 % 38 222 203
30 % 38 222 222
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 2271 Flexibility: Low
Max RMSD: 7.5, Avg RMSD: 2.2
PDBFlex
90 % 4 24 2334
70 % 108 209 97
50 % 142 414 42
40 % 142 414 63
30 % 142 414 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 1694
95 % 4 28 1981 Flexibility: Low
Max RMSD: 3.7, Avg RMSD: 1.7
PDBFlex
90 % 4 28 2031
70 % 4 28 2052
50 % 108 213 128
40 % 142 402 80
30 % 142 402 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 2245
95 % 3 22 2546 Flexibility: Low
Max RMSD: 1.5, Avg RMSD: 1.0
PDBFlex
90 % 3 22 2613
70 % 100 347 50
50 % 100 350 88
40 % 100 350 102
30 % 100 350 116
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 2039 Flexibility: Low
Max RMSD: 2.7, Avg RMSD: 1.5
PDBFlex
90 % 4 27 2089
70 % 4 27 2106
50 % 148 418 47
40 % 148 422 60
30 % 148 423 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 1615
95 % 4 29 1889 Flexibility: Low
Max RMSD: 2.2, Avg RMSD: 1.2
PDBFlex
90 % 4 29 1933
70 % 4 29 1949
50 % 108 214 127
40 % 143 414 62
30 % 143 414 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 2010
95 % 4 24 2313 Flexibility: Low
Max RMSD: 2.3, Avg RMSD: 1.4
PDBFlex
90 % 4 24 2377
70 % 110 211 94
50 % 148 412 43
40 % 148 412 64
30 % 148 412 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 46409
95 % 1 2 38681 Flexibility: Low
Max RMSD: 0.7, Avg RMSD: 0.7
PDBFlex
90 % 1 2 36865
70 % 1 2 32657
50 % 1 2 27796
40 % 1 2 24381
30 % 1 2 20340
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 17097
95 % 1 5 15845 Flexibility: No
Max RMSD: 0.6, Avg RMSD: 0.4
PDBFlex
90 % 1 5 15502
70 % 1 5 14434
50 % 91 156 173
40 % 118 323 103
30 % 118 326 117
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 2271
95 % 4 21 2579 Flexibility: Low
Max RMSD: 3.8, Avg RMSD: 2.1
PDBFlex
90 % 4 21 2649
70 % 20 65 566
50 % 50 253 155
40 % 50 256 163
30 % 50 259 178

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 3 A 50S ribosomal protein L2 1299
2 4IO9 3 A 50S ribosomal protein L2 1299
3 5DM6 2 A 50S ribosomal protein L2 1299
4 1NKW 3 A 50S ribosomal protein L2 1299
5 5JVG 3 A 50S ribosomal protein L2 1299
6 4IOC 3 A 50S ribosomal protein L2 1299
7 5JVH 3 A 50S ribosomal protein L2 1299
8 2ZJR 3 A 50S ribosomal protein L2 1299
9 3PIO 3 A 50S ribosomal protein L2 1299
10 5DM7 2 A 50S ribosomal protein L2 1299
11 4WFN 1 A 50S ribosomal protein L2 1299
12 4U67 1 A 50S ribosomal protein L2 1299
13 3PIP 3 A 50S ribosomal protein L2 1299
14 3CF5 6 A 50S RIBOSOMAL PROTEIN L2 1299
15 3DLL 3 A 50S ribosomal protein L2 1299
16 1NWY 3 A ribosomal protein L2 1299
17 1SM1 8 A 50S RIBOSOMAL PROTEIN L2 1299
18 2ZJQ 3 A 50S ribosomal protein L2 1299
19 1NWX 3 A ribosomal protein L2 1299
20 1XBP 3 A 50S ribosomal protein L2 1299
21 2ZJP 6 A 50S RIBOSOMAL PROTEIN L2 1299
22 4V49 25 BA 50S ribosomal protein L2 562
23 4V4A 23 BA 50S ribosomal protein L2 562
24 4V4G 24 BD, DD, FD, HD, JD 50S ribosomal protein L2 562