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 3217
95 % 3 19 3521 Flexibility: Low
Max RMSD: 1.9, Avg RMSD: 1.2
PDBFlex
90 % 3 19 3593
70 % 3 19 3536
50 % 3 19 3350
40 % 3 19 3229
30 % 3 19 3052
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 1928
95 % 4 24 2235 Flexibility: Low
Max RMSD: 1.6, Avg RMSD: 0.8
PDBFlex
90 % 4 24 2289
70 % 113 231 82
50 % 141 398 38
40 % 237 604 21
30 % 237 604 35
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 1872
95 % 4 24 2176 Flexibility: Low
Max RMSD: 8.4, Avg RMSD: 2.9
PDBFlex
90 % 4 24 2232
70 % 4 24 2247
50 % 140 380 54
40 % 140 380 74
30 % 140 380 88
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 1651
95 % 4 27 1953 Flexibility: Low
Max RMSD: 5.2, Avg RMSD: 2.7
PDBFlex
90 % 4 27 1994
70 % 107 202 96
50 % 140 386 47
40 % 140 386 66
30 % 140 386 82
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 1946
95 % 4 24 2260 Flexibility: Low
Max RMSD: 1.7, Avg RMSD: 0.9
PDBFlex
90 % 4 24 2315
70 % 4 24 2341
50 % 141 379 44
40 % 141 386 56
30 % 141 388 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 2104
95 % 4 24 2259 Flexibility: Low
Max RMSD: 2.8, Avg RMSD: 1.6
PDBFlex
90 % 4 24 2314
70 % 4 24 2319
50 % 140 381 53
40 % 140 381 72
30 % 140 381 87
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 3195
95 % 3 19 3496 Flexibility: Medium
Max RMSD: 7.0, Avg RMSD: 3.0
PDBFlex
90 % 3 19 3564
70 % 3 19 3504
50 % 3 19 3417
40 % 3 19 3277
30 % 3 19 3031
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 1586
95 % 4 28 1863 Flexibility: Low
Max RMSD: 1.4, Avg RMSD: 0.8
PDBFlex
90 % 4 28 1903
70 % 4 28 1927
50 % 141 385 43
40 % 141 393 55
30 % 141 393 72
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 1613
95 % 4 28 1894 Flexibility: Medium
Max RMSD: 7.9, Avg RMSD: 3.7
PDBFlex
90 % 4 28 1933
70 % 4 28 1959
50 % 112 221 118
40 % 140 380 75
30 % 140 380 90
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 1612
95 % 4 30 1764 Flexibility: Low
Max RMSD: 2.5, Avg RMSD: 1.1
PDBFlex
90 % 4 30 1803
70 % 4 30 1815
50 % 4 30 1845
40 % 4 30 1826
30 % 4 30 1773
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 1679
95 % 4 26 1984 Flexibility: Low
Max RMSD: 2.0, Avg RMSD: 1.1
PDBFlex
90 % 4 26 2024
70 % 4 26 2038
50 % 107 201 129
40 % 207 465 42
30 % 207 465 62
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 1797
95 % 4 25 2127 Flexibility: Low
Max RMSD: 3.3, Avg RMSD: 1.6
PDBFlex
90 % 4 25 2179
70 % 4 25 2193
50 % 140 383 50
40 % 140 385 67
30 % 140 385 84
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 2196
95 % 3 25 2507 Flexibility: Low
Max RMSD: 6.5, Avg RMSD: 1.7
PDBFlex
90 % 3 25 2584
70 % 3 25 2571
50 % 3 25 2551
40 % 3 25 2506
30 % 3 25 2341
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 1517
95 % 4 29 1791 Flexibility: Medium
Max RMSD: 11.9, Avg RMSD: 5.0
PDBFlex
90 % 4 29 1833
70 % 33 186 172
50 % 142 383 48
40 % 142 383 68
30 % 142 383 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 1678
95 % 4 26 1966 Flexibility: Low
Max RMSD: 2.8, Avg RMSD: 1.5
PDBFlex
90 % 4 26 2006
70 % 4 26 2022
50 % 4 26 2068
40 % 4 26 2038
30 % 207 451 66
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 1829
95 % 4 24 2141 Flexibility: Low
Max RMSD: 1.8, Avg RMSD: 0.9
PDBFlex
90 % 4 24 2192
70 % 4 24 2208
50 % 37 203 191
40 % 141 386 62
30 % 141 386 78
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 3813
95 % 1 12 4183 Flexibility: No
Max RMSD: 0.5, Avg RMSD: 0.4
PDBFlex
90 % 1 12 4231
70 % 1 12 4153
50 % 103 236 123
40 % 103 247 140
30 % 103 248 149
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 1270
95 % 4 34 1502 Flexibility: Low
Max RMSD: 1.5, Avg RMSD: 0.9
PDBFlex
90 % 4 34 1522
70 % 4 34 1546
50 % 140 376 63
40 % 140 382 69
30 % 140 382 85
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 12645
95 % 1 6 13227 Flexibility: Low
Max RMSD: 0.5, Avg RMSD: 0.5
PDBFlex
90 % 1 6 11504
70 % 1 6 10858
50 % 1 6 9764
40 % 1 6 8841
30 % 1 6 7628
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 1609
95 % 4 28 1888 Flexibility: Low
Max RMSD: 1.8, Avg RMSD: 1.1
PDBFlex
90 % 4 28 1929
70 % 32 182 176
50 % 37 205 190
40 % 37 205 207
30 % 37 205 225
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 1876
95 % 4 24 2179 Flexibility: Low
Max RMSD: 7.5, Avg RMSD: 2.2
PDBFlex
90 % 4 24 2234
70 % 108 199 98
50 % 141 387 45
40 % 141 387 64
30 % 141 387 80
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 1610
95 % 4 28 1889 Flexibility: Low
Max RMSD: 3.7, Avg RMSD: 1.7
PDBFlex
90 % 4 28 1930
70 % 4 28 1955
50 % 108 203 128
40 % 141 375 82
30 % 141 375 96
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 2140
95 % 3 22 2452 Flexibility: Low
Max RMSD: 1.5, Avg RMSD: 1.0
PDBFlex
90 % 3 22 2524
70 % 100 321 48
50 % 100 324 87
40 % 100 324 107
30 % 100 324 121
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 1631
95 % 4 27 1917 Flexibility: Low
Max RMSD: 2.7, Avg RMSD: 1.5
PDBFlex
90 % 4 27 1956
70 % 4 27 1977
50 % 146 390 49
40 % 146 394 61
30 % 146 395 77
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 1528
95 % 4 29 1803 Flexibility: Low
Max RMSD: 2.2, Avg RMSD: 1.2
PDBFlex
90 % 4 29 1842
70 % 4 29 1859
50 % 108 204 126
40 % 142 387 63
30 % 142 387 79
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 1912
95 % 4 24 2219 Flexibility: Low
Max RMSD: 2.3, Avg RMSD: 1.4
PDBFlex
90 % 4 24 2272
70 % 110 201 95
50 % 147 385 46
40 % 147 385 65
30 % 147 385 81
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 44906
95 % 1 2 37466 Flexibility: Low
Max RMSD: 0.7, Avg RMSD: 0.7
PDBFlex
90 % 1 2 35751
70 % 1 2 31739
50 % 1 2 26983
40 % 1 2 23665
30 % 1 2 19716
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 16407
95 % 1 5 15227 Flexibility: No
Max RMSD: 0.6, Avg RMSD: 0.4
PDBFlex
90 % 1 5 14917
70 % 1 5 13955
50 % 91 150 175
40 % 117 304 105
30 % 117 307 118
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 2165
95 % 4 21 2537 Flexibility: Low
Max RMSD: 3.8, Avg RMSD: 2.1
PDBFlex
90 % 4 21 2557
70 % 20 64 547
50 % 49 240 153
40 % 49 243 164
30 % 49 246 177

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