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 3066
95 % 3 19 3370 Flexibility: Low
Max RMSD: 1.9, Avg RMSD: 1.3
PDBFlex
90 % 3 19 3427
70 % 3 19 3384
50 % 3 19 3299
40 % 3 19 3173
30 % 3 19 2952
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 1845
95 % 4 24 2140 Flexibility: Low
Max RMSD: 1.3, Avg RMSD: 0.8
PDBFlex
90 % 4 24 2187
70 % 102 212 93
50 % 130 363 55
40 % 225 557 21
30 % 225 557 34
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 1780
95 % 4 24 2084 Flexibility: Low
Max RMSD: 3.4, Avg RMSD: 1.9
PDBFlex
90 % 4 24 2134
70 % 4 24 2149
50 % 129 346 68
40 % 129 346 90
30 % 129 346 100
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 1563
95 % 4 27 1855 Flexibility: Low
Max RMSD: 5.2, Avg RMSD: 2.7
PDBFlex
90 % 4 27 1895
70 % 96 183 101
50 % 129 354 60
40 % 129 354 77
30 % 129 354 87
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 1864
95 % 4 24 2159 Flexibility: Low
Max RMSD: 1.7, Avg RMSD: 0.9
PDBFlex
90 % 4 24 2210
70 % 4 24 2237
50 % 130 345 62
40 % 130 351 74
30 % 130 353 83
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 1976
95 % 4 24 2118 Flexibility: Low
Max RMSD: 2.8, Avg RMSD: 1.5
PDBFlex
90 % 4 24 2164
70 % 4 24 2179
50 % 129 348 67
40 % 129 348 87
30 % 129 348 96
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 3059
95 % 3 19 3361 Flexibility: Medium
Max RMSD: 6.7, Avg RMSD: 3.3
PDBFlex
90 % 3 19 3418
70 % 3 19 3372
50 % 3 19 3289
40 % 3 19 3164
30 % 3 19 2947
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 1509
95 % 4 28 1769 Flexibility: Low
Max RMSD: 1.4, Avg RMSD: 0.8
PDBFlex
90 % 4 28 1809
70 % 4 28 1835
50 % 130 351 59
40 % 130 358 71
30 % 130 358 84
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 1532
95 % 4 28 1799 Flexibility: Medium
Max RMSD: 7.9, Avg RMSD: 3.5
PDBFlex
90 % 4 28 1839
70 % 4 28 1871
50 % 101 202 127
40 % 129 346 91
30 % 129 346 101
Entity #19 | Chains: Q
50S ribosomal protein L22 protein, length: 134 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 4 28 1531
95 % 4 30 1667
90 % 4 30 1708
70 % 4 30 1727
50 % 4 30 1758
40 % 4 30 1744
30 % 4 30 1703
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
100 % 4 26 1592
95 % 4 26 1883
90 % 4 26 1925
70 % 4 26 1952
50 % 96 182 141
40 % 196 430 45
30 % 196 430 64
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 1720
95 % 4 25 2044 Flexibility: Low
Max RMSD: 3.3, Avg RMSD: 1.6
PDBFlex
90 % 4 25 2094
70 % 4 25 2109
50 % 129 349 65
40 % 129 351 84
30 % 129 351 94
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 2100
95 % 3 25 2393 Flexibility: Low
Max RMSD: 6.5, Avg RMSD: 1.8
PDBFlex
90 % 3 25 2465
70 % 3 25 2458
50 % 3 25 2451
40 % 3 25 2412
30 % 3 25 2270
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 1441
95 % 4 29 1696 Flexibility: Medium
Max RMSD: 11.9, Avg RMSD: 5.1
PDBFlex
90 % 4 29 1737
70 % 33 172 172
50 % 131 350 63
40 % 131 350 81
30 % 131 350 91
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 1591
95 % 4 26 1865 Flexibility: Low
Max RMSD: 2.8, Avg RMSD: 1.5
PDBFlex
90 % 4 26 1907
70 % 4 26 1936
50 % 4 26 1977
40 % 4 26 1952
30 % 196 417 69
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 1752
95 % 4 24 2059 Flexibility: Low
Max RMSD: 1.8, Avg RMSD: 0.9
PDBFlex
90 % 4 24 2107
70 % 4 24 2124
50 % 37 188 195
40 % 130 352 79
30 % 130 352 90
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 3644
95 % 1 12 4008 Flexibility: No
Max RMSD: 0.5, Avg RMSD: 0.4
PDBFlex
90 % 1 12 4044
70 % 1 12 3979
50 % 92 208 136
40 % 92 219 148
30 % 92 219 167
Entity #27 | Chains: Z
50S ribosomal protein L32 protein, length: 60 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 4 34 1214
95 % 4 34 1445
90 % 4 34 1471
70 % 4 34 1478
50 % 129 342 70
40 % 129 348 88
30 % 129 348 97
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 12089
95 % 1 6 12695 Flexibility: Low
Max RMSD: 0.5, Avg RMSD: 0.5
PDBFlex
90 % 1 6 11446
70 % 1 6 10828
50 % 1 6 9425
40 % 1 6 8539
30 % 1 6 7382
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 1503
95 % 4 28 1765 Flexibility: Low
Max RMSD: 1.6, Avg RMSD: 1.0
PDBFlex
90 % 4 28 1804
70 % 32 167 174
50 % 37 190 194
40 % 37 190 212
30 % 37 190 229
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 1791
95 % 4 24 2090 Flexibility: Low
Max RMSD: 7.5, Avg RMSD: 2.3
PDBFlex
90 % 4 24 2138
70 % 97 180 102
50 % 130 351 64
40 % 130 351 85
30 % 130 351 95
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 1529
95 % 4 28 1795 Flexibility: Low
Max RMSD: 3.7, Avg RMSD: 1.7
PDBFlex
90 % 4 28 1836
70 % 4 28 1869
50 % 97 184 140
40 % 130 344 92
30 % 130 344 103
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 2041
95 % 3 22 2338 Flexibility: Low
Max RMSD: 1.4, Avg RMSD: 1.0
PDBFlex
90 % 3 22 2359
70 % 92 296 50
50 % 92 299 91
40 % 92 299 113
30 % 92 299 126
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 1560
95 % 4 27 1848 Flexibility: Low
Max RMSD: 2.6, Avg RMSD: 1.4
PDBFlex
90 % 4 27 1887
70 % 4 27 1923
50 % 135 355 66
40 % 135 358 82
30 % 135 359 89
Entity #5 | Chains: C
50S ribosomal protein L4 protein, length: 205 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 4 29 1450
95 % 4 29 1709
90 % 4 29 1749
70 % 4 29 1773
50 % 97 185 139
40 % 131 352 83
30 % 131 352 93
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 1824
95 % 4 24 2123 Flexibility: Low
Max RMSD: 2.3, Avg RMSD: 1.4
PDBFlex
90 % 4 24 2168
70 % 99 182 100
50 % 136 353 61
40 % 136 353 78
30 % 136 353 88
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 43297
95 % 1 2 36181 Flexibility: Low
Max RMSD: 0.7, Avg RMSD: 0.7
PDBFlex
90 % 1 2 34576
70 % 1 2 30762
50 % 1 2 26219
40 % 1 2 23002
30 % 1 2 19185
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 15709
95 % 1 5 14620 Flexibility: No
Max RMSD: 0.6, Avg RMSD: 0.5
PDBFlex
90 % 1 5 14349
70 % 1 5 13460
50 % 80 131 186
40 % 106 276 114
30 % 106 279 128
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 2064
95 % 4 21 2360 Flexibility: Low
Max RMSD: 3.8, Avg RMSD: 2.2
PDBFlex
90 % 4 21 2433
70 % 19 62 548
50 % 48 229 149
40 % 48 232 160
30 % 48 235 177

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 4 B 50S ribosomal protein L3 1299
2 4IO9 4 B 50S ribosomal protein L3 1299
3 5DM6 3 B 50S ribosomal protein L3 1299
4 1NKW 4 B 50S ribosomal protein L3 1299
5 5JVG 4 B 50S ribosomal protein L3 1299
6 4IOC 4 B 50S ribosomal protein L3 1299
7 5JVH 4 B 50S ribosomal protein L3 deinococcus 1299
8 2ZJR 4 B 50S ribosomal protein L3 1299
9 3PIO 4 B 50S ribosomal protein L3 1299
10 5DM7 3 B 50S ribosomal protein L3 1299
11 4WFN 2 B 50S ribosomal protein L3 1299
12 4U67 2 B 50S ribosomal protein L3 1299
13 3PIP 4 B 50S ribosomal protein L3 1299
14 3CF5 7 B 50S RIBOSOMAL PROTEIN L3 1299
15 3DLL 4 B 50S ribosomal protein L3 1299
16 1NWY 4 B ribosomal protein L3 1299
17 1SM1 9 B 50S RIBOSOMAL PROTEIN L3 1299
18 2OGO 2 B 50S ribosomal protein L3 1299
19 2OGM 2 B 50S ribosomal protein L3 1299
20 2OGN 2 B 50S ribosomal protein L3 1299
21 2ZJQ 4 B 50S ribosomal protein L3 1299
22 1NWX 4 B ribosomal protein L3 1299
23 1XBP 4 B 50S ribosomal protein L3 1299
24 2ZJP 7 B 50S RIBOSOMAL PROTEIN L3 1299
25 4V49 26 BB 50S ribosomal protein L3 562
26 4V4A 24 BB 50S ribosomal protein L3 562
27 4V4G 25 BE, DE, FE, HE, JE 50S ribosomal protein L3 562