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 2785
95 % 3 19 3443 Flexibility: Low
Max RMSD: 1.9, Avg RMSD: 1.3
PDBFlex
90 % 3 19 3500
70 % 3 19 3459
50 % 3 19 3377
40 % 3 19 3275
30 % 3 19 3073
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 1658
95 % 4 24 2205 Flexibility: Low
Max RMSD: 1.3, Avg RMSD: 0.8
PDBFlex
90 % 4 24 2261
70 % 110 225 83
50 % 138 379 43
40 % 234 580 20
30 % 234 580 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 1654
95 % 4 24 2197 Flexibility: Low
Max RMSD: 3.4, Avg RMSD: 1.9
PDBFlex
90 % 4 24 2251
70 % 4 24 2247
50 % 137 361 61
40 % 137 361 82
30 % 233 555 41
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 1411
95 % 4 27 1900 Flexibility: Low
Max RMSD: 5.2, Avg RMSD: 2.7
PDBFlex
90 % 4 27 1944
70 % 104 196 97
50 % 137 371 48
40 % 137 371 65
30 % 137 371 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 1667
95 % 4 24 2213 Flexibility: Low
Max RMSD: 1.7, Avg RMSD: 0.9
PDBFlex
90 % 4 24 2270
70 % 4 24 2266
50 % 133 341 66
40 % 138 367 60
30 % 138 369 76
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 1825
95 % 4 24 2214 Flexibility: Low
Max RMSD: 2.8, Avg RMSD: 1.5
PDBFlex
90 % 4 24 2271
70 % 4 24 2267
50 % 137 364 58
40 % 137 364 79
30 % 137 364 93
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 2789
95 % 3 19 3446 Flexibility: Medium
Max RMSD: 6.7, Avg RMSD: 3.3
PDBFlex
90 % 3 19 3503
70 % 3 19 3464
50 % 3 19 3381
40 % 3 19 3277
30 % 3 19 3076
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 1374
95 % 4 28 1850 Flexibility: Low
Max RMSD: 1.4, Avg RMSD: 0.8
PDBFlex
90 % 4 28 1890
70 % 4 28 1907
50 % 138 366 55
40 % 138 374 58
30 % 138 374 75
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 1379
95 % 4 28 1855 Flexibility: Medium
Max RMSD: 7.9, Avg RMSD: 3.5
PDBFlex
90 % 4 28 1894
70 % 4 28 1913
50 % 109 215 118
40 % 137 361 83
30 % 137 361 95
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 1369
95 % 4 30 1706
90 % 4 30 1746
70 % 4 30 1756
50 % 4 30 1787
40 % 4 30 1787
30 % 4 30 1746
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 1501
95 % 4 26 2027
90 % 4 26 2076
70 % 4 26 2085
50 % 104 195 132
40 % 137 367 74
30 % 204 446 65
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 1541
95 % 4 25 2081 Flexibility: Low
Max RMSD: 3.3, Avg RMSD: 1.6
PDBFlex
90 % 4 25 2133
70 % 4 25 2140
50 % 137 364 59
40 % 137 366 76
30 % 137 366 92
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 1865
95 % 3 25 2434 Flexibility: Low
Max RMSD: 6.5, Avg RMSD: 1.8
PDBFlex
90 % 3 25 2497
70 % 3 25 2503
50 % 3 25 2481
40 % 3 25 2446
30 % 3 25 2336
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 1309
95 % 4 29 1767 Flexibility: Medium
Max RMSD: 11.9, Avg RMSD: 5.1
PDBFlex
90 % 4 29 1807
70 % 33 175 173
50 % 139 366 56
40 % 139 366 72
30 % 139 366 89
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 1507
95 % 4 26 2035 Flexibility: Low
Max RMSD: 2.8, Avg RMSD: 1.5
PDBFlex
90 % 4 26 2084
70 % 4 26 2092
50 % 4 26 2094
40 % 4 26 2086
30 % 204 432 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 1684
95 % 4 24 2233 Flexibility: Low
Max RMSD: 1.8, Avg RMSD: 0.9
PDBFlex
90 % 4 24 2289
70 % 4 24 2281
50 % 37 190 198
40 % 138 367 73
30 % 138 367 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 3638
95 % 1 12 4433 Flexibility: No
Max RMSD: 0.5, Avg RMSD: 0.4
PDBFlex
90 % 1 12 4473
70 % 1 12 4382
50 % 100 223 126
40 % 100 234 140
30 % 100 235 147
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 1100
95 % 4 34 1483
90 % 4 34 1507
70 % 4 34 1506
50 % 109 215 121
40 % 137 363 80
30 % 137 363 94
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 14645
95 % 1 6 13854 Flexibility: Low
Max RMSD: 0.5, Avg RMSD: 0.5
PDBFlex
90 % 1 6 13623
70 % 1 6 12791
50 % 1 6 11405
40 % 1 6 10331
30 % 1 6 9004
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 1387
95 % 4 28 1861 Flexibility: Low
Max RMSD: 1.6, Avg RMSD: 1.0
PDBFlex
90 % 4 28 1901
70 % 32 169 176
50 % 37 192 195
40 % 37 192 210
30 % 37 192 220
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 % 3 22 1784
95 % 4 24 2154 Flexibility: Low
Max RMSD: 7.5, Avg RMSD: 2.3
PDBFlex
90 % 4 24 2206
70 % 105 193 98
50 % 138 370 49
40 % 234 557 22
30 % 234 557 39
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 1386
95 % 4 28 1860 Flexibility: Low
Max RMSD: 3.7, Avg RMSD: 1.7
PDBFlex
90 % 4 28 1899
70 % 4 28 1918
50 % 105 197 130
40 % 138 359 84
30 % 138 359 97
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 1833
95 % 3 22 2402 Flexibility: Low
Max RMSD: 1.4, Avg RMSD: 1.0
PDBFlex
90 % 3 22 2468
70 % 72 170 148
50 % 100 315 87
40 % 100 315 106
30 % 100 315 119
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 1405
95 % 4 27 1890 Flexibility: Low
Max RMSD: 2.6, Avg RMSD: 1.4
PDBFlex
90 % 4 27 1932
70 % 4 27 1948
50 % 143 371 57
40 % 143 375 68
30 % 143 376 82
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 1294
95 % 4 29 1749
90 % 4 29 1791
70 % 4 29 1800
50 % 105 198 127
40 % 139 367 75
30 % 139 368 91
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 1647
95 % 4 24 2190 Flexibility: Low
Max RMSD: 2.3, Avg RMSD: 1.4
PDBFlex
90 % 4 24 2243
70 % 107 195 95
50 % 144 368 54
40 % 144 368 70
30 % 144 368 85
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 42513
95 % 1 2 32295 Flexibility: Low
Max RMSD: 0.7, Avg RMSD: 0.7
PDBFlex
90 % 1 2 30890
70 % 1 2 27581
50 % 1 2 23506
40 % 1 2 20685
30 % 1 2 17514
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 16330
95 % 1 5 15219 Flexibility: No
Max RMSD: 0.6, Avg RMSD: 0.5
PDBFlex
90 % 1 5 14937
70 % 1 5 14004
50 % 88 144 178
40 % 114 286 111
30 % 114 294 120
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 % 3 19 2195
95 % 4 21 2460 Flexibility: Low
Max RMSD: 3.8, Avg RMSD: 2.2
PDBFlex
90 % 4 21 2522
70 % 20 63 546
50 % 49 232 150
40 % 49 235 161
30 % 49 238 168

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 1NKW 28 1 50S ribosomal protein L33 1299
2 1SM1 2 1 50S RIBOSOMAL PROTEIN L33 1299
3 4V4P 30 A6 50S ribosomal protein L33 274
4 4V4R 52 B6 50S ribosomal protein L33 274
5 4V4S 52 B6 50S ribosomal protein L33 274
6 4V4T 51 B6 50S ribosomal protein L33 274