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 3315
95 % 3 19 3617 Flexibility: Low
Max RMSD: 1.9, Avg RMSD: 1.2
PDBFlex
90 % 3 19 3684
70 % 3 19 3628
50 % 3 19 3428
40 % 3 19 3303
30 % 3 19 3123
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 1984
95 % 4 24 2290 Flexibility: Low
Max RMSD: 1.6, Avg RMSD: 0.8
PDBFlex
90 % 4 24 2349
70 % 113 241 83
50 % 141 415 38
40 % 237 625 23
30 % 237 625 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 1979
95 % 4 24 2284 Flexibility: Low
Max RMSD: 8.4, Avg RMSD: 2.9
PDBFlex
90 % 4 24 2342
70 % 4 24 2337
50 % 140 397 58
40 % 140 397 74
30 % 140 397 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 1705
95 % 4 27 2009 Flexibility: Low
Max RMSD: 5.2, Avg RMSD: 2.7
PDBFlex
90 % 4 27 2053
70 % 107 205 96
50 % 140 403 45
40 % 140 403 66
30 % 140 403 81
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 2002
95 % 4 24 2316 Flexibility: Low
Max RMSD: 1.7, Avg RMSD: 0.9
PDBFlex
90 % 4 24 2377
70 % 4 24 2389
50 % 141 399 41
40 % 141 399 58
30 % 141 401 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 2163
95 % 4 24 2315 Flexibility: Low
Max RMSD: 2.8, Avg RMSD: 1.6
PDBFlex
90 % 4 24 2376
70 % 4 24 2369
50 % 140 398 53
40 % 140 398 71
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 3295
95 % 3 19 3587 Flexibility: Medium
Max RMSD: 7.0, Avg RMSD: 3.0
PDBFlex
90 % 3 19 3652
70 % 3 19 3596
50 % 3 19 3498
40 % 3 19 3360
30 % 3 19 3101
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 1637
95 % 4 28 1920 Flexibility: Low
Max RMSD: 1.4, Avg RMSD: 0.8
PDBFlex
90 % 4 28 1963
70 % 4 28 1985
50 % 141 402 42
40 % 141 410 55
30 % 141 410 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 1667
95 % 4 28 1953 Flexibility: Medium
Max RMSD: 7.9, Avg RMSD: 3.7
PDBFlex
90 % 4 28 1993
70 % 4 28 2019
50 % 112 226 120
40 % 140 397 75
30 % 140 397 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 1666
95 % 4 30 1810 Flexibility: Low
Max RMSD: 2.5, Avg RMSD: 1.1
PDBFlex
90 % 4 30 1852
70 % 4 30 1867
50 % 4 30 1900
40 % 4 30 1882
30 % 4 30 1824
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 1735
95 % 4 26 2044 Flexibility: Low
Max RMSD: 2.0, Avg RMSD: 1.1
PDBFlex
90 % 4 26 2089
70 % 4 26 2104
50 % 112 235 114
40 % 207 482 42
30 % 207 482 61
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 1858
95 % 4 25 2188 Flexibility: Low
Max RMSD: 3.3, Avg RMSD: 1.6
PDBFlex
90 % 4 25 2245
70 % 4 25 2256
50 % 140 400 49
40 % 140 402 67
30 % 140 402 82
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 2266
95 % 3 25 2567 Flexibility: Low
Max RMSD: 6.5, Avg RMSD: 1.7
PDBFlex
90 % 3 25 2639
70 % 3 25 2629
50 % 3 25 2615
40 % 3 25 2570
30 % 3 25 2395
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 1571
95 % 4 29 1841 Flexibility: Medium
Max RMSD: 11.9, Avg RMSD: 5.0
PDBFlex
90 % 4 29 1884
70 % 33 193 171
50 % 142 400 47
40 % 142 400 68
30 % 142 400 83
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 1734
95 % 4 26 2043 Flexibility: Low
Max RMSD: 2.8, Avg RMSD: 1.5
PDBFlex
90 % 4 26 2088
70 % 4 26 2103
50 % 4 26 2126
40 % 4 26 2099
30 % 207 464 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 1888
95 % 4 24 2203 Flexibility: Low
Max RMSD: 1.8, Avg RMSD: 0.9
PDBFlex
90 % 4 24 2260
70 % 4 24 2270
50 % 37 217 196
40 % 141 403 61
30 % 141 403 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 3930
95 % 1 12 4301 Flexibility: No
Max RMSD: 0.5, Avg RMSD: 0.4
PDBFlex
90 % 1 12 4350
70 % 1 12 4265
50 % 103 243 122
40 % 103 260 137
30 % 103 261 149
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 1336
95 % 4 34 1575 Flexibility: Low
Max RMSD: 1.5, Avg RMSD: 0.9
PDBFlex
90 % 4 34 1600
70 % 4 34 1610
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 12998
95 % 1 6 13586 Flexibility: Low
Max RMSD: 0.5, Avg RMSD: 0.5
PDBFlex
90 % 1 6 11807
70 % 1 6 11165
50 % 1 6 10013
40 % 1 6 9056
30 % 1 6 7802
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 1663
95 % 4 28 1947 Flexibility: Low
Max RMSD: 1.8, Avg RMSD: 1.1
PDBFlex
90 % 4 28 1989
70 % 32 189 176
50 % 37 219 193
40 % 37 219 205
30 % 37 219 222
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 1931
95 % 4 24 2235 Flexibility: Low
Max RMSD: 7.5, Avg RMSD: 2.2
PDBFlex
90 % 4 24 2293
70 % 108 202 98
50 % 141 404 43
40 % 141 404 64
30 % 141 404 79
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 1664
95 % 4 28 1948 Flexibility: Low
Max RMSD: 3.7, Avg RMSD: 1.7
PDBFlex
90 % 4 28 1990
70 % 4 28 2015
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 2206
95 % 3 22 2508 Flexibility: Low
Max RMSD: 1.5, Avg RMSD: 1.0
PDBFlex
90 % 3 22 2575
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 1682
95 % 4 27 2002 Flexibility: Low
Max RMSD: 2.7, Avg RMSD: 1.5
PDBFlex
90 % 4 27 2045
70 % 4 27 2070
50 % 146 407 48
40 % 146 411 59
30 % 146 412 74
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 1582
95 % 4 29 1855 Flexibility: Low
Max RMSD: 2.2, Avg RMSD: 1.2
PDBFlex
90 % 4 29 1896
70 % 4 29 1911
50 % 108 207 127
40 % 142 404 63
30 % 142 404 78
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 1968
95 % 4 24 2274 Flexibility: Low
Max RMSD: 2.3, Avg RMSD: 1.4
PDBFlex
90 % 4 24 2332
70 % 110 204 95
50 % 147 402 44
40 % 147 402 65
30 % 147 402 80
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 45947
95 % 1 2 38307 Flexibility: Low
Max RMSD: 0.7, Avg RMSD: 0.7
PDBFlex
90 % 1 2 36531
70 % 1 2 32386
50 % 1 2 27541
40 % 1 2 24158
30 % 1 2 20148
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 16896
95 % 1 5 15668 Flexibility: No
Max RMSD: 0.6, Avg RMSD: 0.4
PDBFlex
90 % 1 5 15333
70 % 1 5 14296
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 2233
95 % 4 21 2542 Flexibility: Low
Max RMSD: 3.8, Avg RMSD: 2.1
PDBFlex
90 % 4 21 2613
70 % 20 65 558
50 % 49 251 152
40 % 49 254 161
30 % 49 257 177

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 16 N 50S ribosomal protein L20 1299
2 4IO9 16 N 50S ribosomal protein L20 1299
3 5DM6 15 N 50S ribosomal protein L20 1299
4 1NKW 17 O 50S ribosomal protein L20 1299
5 5JVG 16 N 50S ribosomal protein L20 1299
6 4IOC 16 N 50S ribosomal protein L20 1299
7 5JVH 15 N 50S ribosomal protein L20 1299
8 2ZJR 16 N 50S ribosomal protein L20 1299
9 3PIO 16 N 50S ribosomal protein L20 1299
10 5DM7 15 N 50S ribosomal protein L20 1299
11 4WFN 13 N 50S ribosomal protein L20 1299
12 4U67 13 N 50S ribosomal protein L20 1299
13 3PIP 16 N 50S ribosomal protein L20 1299
14 3CF5 19 N 50S RIBOSOMAL PROTEIN L20 1299
15 3DLL 16 N 50S ribosomal protein L20 1299
16 1NWY 17 O ribosomal protein L20 1299
17 1SM1 22 O 50S RIBOSOMAL PROTEIN L20 1299
18 2ZJQ 16 N 50S ribosomal protein L20 1299
19 1NWX 17 O ribosomal protein L20 1299
20 1XBP 17 O 50S ribosomal protein L20 1299
21 2ZJP 19 N 50S RIBOSOMAL PROTEIN L20 1299
22 4V4P 25 A1 50S ribosomal protein L20 274
23 4V4R 45 BU 50S ribosomal protein L20 274
24 4V4S 45 BU 50S ribosomal protein L20 274
25 4V4T 44 BU 50S ribosomal protein L20 274
26 4V49 39 BO 50S ribosomal protein L20 562
27 4V4A 37 BO 50S ribosomal protein L20 562
28 4V4G 38 BR, DR, FR, HR, JR 50S ribosomal protein L20 562