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 3151
95 % 3 19 3458 Flexibility: Low
Max RMSD: 1.9, Avg RMSD: 1.3
PDBFlex
90 % 3 19 3522
70 % 3 19 3469
50 % 3 19 3388
40 % 3 19 3254
30 % 3 19 3012
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 1898
95 % 4 24 2196 Flexibility: Low
Max RMSD: 1.3, Avg RMSD: 0.8
PDBFlex
90 % 4 24 2256
70 % 111 228 83
50 % 139 388 42
40 % 235 589 21
30 % 235 589 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 1840
95 % 4 24 2142 Flexibility: Low
Max RMSD: 3.4, Avg RMSD: 1.9
PDBFlex
90 % 4 24 2199
70 % 4 24 2208
50 % 138 370 56
40 % 138 370 74
30 % 138 370 92
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 1628
95 % 4 27 1935 Flexibility: Low
Max RMSD: 5.2, Avg RMSD: 2.7
PDBFlex
90 % 4 27 1978
70 % 105 199 98
50 % 138 380 44
40 % 138 380 62
30 % 138 380 77
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 1917
95 % 4 24 2219 Flexibility: Low
Max RMSD: 1.7, Avg RMSD: 0.9
PDBFlex
90 % 4 24 2280
70 % 4 24 2301
50 % 139 369 49
40 % 139 376 58
30 % 139 378 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 2045
95 % 4 24 2218 Flexibility: Low
Max RMSD: 2.8, Avg RMSD: 1.5
PDBFlex
90 % 4 24 2279
70 % 4 24 2280
50 % 138 373 53
40 % 138 373 72
30 % 138 373 89
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 3146
95 % 3 19 3449 Flexibility: Medium
Max RMSD: 6.7, Avg RMSD: 3.3
PDBFlex
90 % 3 19 3512
70 % 3 19 3455
50 % 3 19 3375
40 % 3 19 3243
30 % 3 19 3005
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 1564
95 % 4 28 1842 Flexibility: Low
Max RMSD: 1.4, Avg RMSD: 0.8
PDBFlex
90 % 4 28 1882
70 % 4 28 1899
50 % 139 375 47
40 % 139 383 57
30 % 139 383 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 1588
95 % 4 28 1871 Flexibility: Medium
Max RMSD: 7.9, Avg RMSD: 3.5
PDBFlex
90 % 4 28 1911
70 % 4 28 1932
50 % 110 218 120
40 % 138 370 75
30 % 138 370 93
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 1587
95 % 4 30 1730
90 % 4 30 1773
70 % 4 30 1780
50 % 4 30 1812
40 % 4 30 1800
30 % 4 30 1754
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 1658
95 % 4 26 1962
90 % 4 26 2006
70 % 4 26 2015
50 % 105 198 130
40 % 205 455 46
30 % 205 455 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 1769
95 % 4 25 2097 Flexibility: Low
Max RMSD: 3.3, Avg RMSD: 1.6
PDBFlex
90 % 4 25 2153
70 % 4 25 2159
50 % 138 373 52
40 % 138 375 71
30 % 138 375 88
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 2162
95 % 3 25 2464 Flexibility: Low
Max RMSD: 6.5, Avg RMSD: 1.8
PDBFlex
90 % 3 25 2537
70 % 3 25 2532
50 % 3 25 2519
40 % 3 25 2474
30 % 3 25 2318
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 1493
95 % 4 29 1765 Flexibility: Medium
Max RMSD: 11.9, Avg RMSD: 5.1
PDBFlex
90 % 4 29 1809
70 % 33 181 172
50 % 140 375 50
40 % 140 375 68
30 % 140 375 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 1657
95 % 4 26 1944 Flexibility: Low
Max RMSD: 2.8, Avg RMSD: 1.5
PDBFlex
90 % 4 26 1988
70 % 4 26 1999
50 % 4 26 2034
40 % 4 26 2008
30 % 205 441 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 1799
95 % 4 24 2111 Flexibility: Low
Max RMSD: 1.8, Avg RMSD: 0.9
PDBFlex
90 % 4 24 2166
70 % 4 24 2173
50 % 37 196 192
40 % 139 376 69
30 % 139 376 84
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 3762
95 % 1 12 4129 Flexibility: No
Max RMSD: 0.5, Avg RMSD: 0.4
PDBFlex
90 % 1 12 4176
70 % 1 12 4101
50 % 101 232 122
40 % 101 243 140
30 % 101 244 152
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 1251
95 % 4 34 1478
90 % 4 34 1501
70 % 4 34 1511
50 % 138 366 64
40 % 138 372 73
30 % 138 372 91
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 12483
95 % 1 6 13066 Flexibility: Low
Max RMSD: 0.5, Avg RMSD: 0.5
PDBFlex
90 % 1 6 11784
70 % 1 6 11130
50 % 1 6 9670
40 % 1 6 8759
30 % 1 6 7565
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 1584
95 % 4 28 1865 Flexibility: Low
Max RMSD: 1.6, Avg RMSD: 1.0
PDBFlex
90 % 4 28 1907
70 % 32 175 175
50 % 37 198 191
40 % 37 198 210
30 % 37 198 228
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 1844
95 % 4 24 2145 Flexibility: Low
Max RMSD: 7.5, Avg RMSD: 2.3
PDBFlex
90 % 4 24 2201
70 % 106 196 99
50 % 139 379 45
40 % 139 379 65
30 % 139 379 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 1585
95 % 4 28 1866 Flexibility: Low
Max RMSD: 3.7, Avg RMSD: 1.7
PDBFlex
90 % 4 28 1908
70 % 4 28 1928
50 % 106 200 129
40 % 139 368 80
30 % 139 368 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 2100
95 % 3 22 2405 Flexibility: Low
Max RMSD: 1.4, Avg RMSD: 1.0
PDBFlex
90 % 3 22 2478
70 % 100 320 49
50 % 100 323 88
40 % 100 323 107
30 % 100 323 122
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 1604
95 % 4 27 1928 Flexibility: Low
Max RMSD: 2.6, Avg RMSD: 1.4
PDBFlex
90 % 4 27 1970
70 % 4 27 1987
50 % 144 380 51
40 % 144 384 64
30 % 144 385 78
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 1504
95 % 4 29 1781
90 % 4 29 1822
70 % 4 29 1832
50 % 106 201 128
40 % 140 377 70
30 % 140 377 87
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 1881
95 % 4 24 2180 Flexibility: Low
Max RMSD: 2.3, Avg RMSD: 1.4
PDBFlex
90 % 4 24 2237
70 % 108 198 96
50 % 145 377 48
40 % 145 377 66
30 % 145 377 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 44381
95 % 1 2 37052 Flexibility: Low
Max RMSD: 0.7, Avg RMSD: 0.7
PDBFlex
90 % 1 2 35370
70 % 1 2 31441
50 % 1 2 26757
40 % 1 2 23474
30 % 1 2 19561
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 16197
95 % 1 5 15045 Flexibility: No
Max RMSD: 0.6, Avg RMSD: 0.5
PDBFlex
90 % 1 5 14748
70 % 1 5 13804
50 % 89 147 177
40 % 115 300 109
30 % 115 303 123
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 2127
95 % 4 21 2433 Flexibility: Low
Max RMSD: 3.8, Avg RMSD: 2.2
PDBFlex
90 % 4 21 2508
70 % 20 63 552
50 % 49 238 151
40 % 49 241 161
30 % 49 244 176

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 28 2 50S ribosomal protein L34 1299
2 4IO9 28 2 50S ribosomal protein L34 1299
3 5DM6 27 2 50S ribosomal protein L34 1299
4 1NKW 29 2 50S ribosomal protein L34 1299
5 5JVG 28 2 50S ribosomal protein L34 1299
6 4IOC 28 2 50S ribosomal protein L34 1299
7 5JVH 27 2 50S ribosomal protein L34 1299
8 2ZJR 28 2 50S ribosomal protein L34 1299
9 3PIO 28 2 50S ribosomal protein L34 1299
10 5DM7 27 2 50S ribosomal protein L34 1299
11 4WFN 25 2 50S ribosomal protein L34 1299
12 4U67 25 2 50S ribosomal protein L34 1299
13 3PIP 28 2 50S ribosomal protein L34 1299
14 3CF5 2 2 50S RIBOSOMAL PROTEIN L34 1299
15 3DLL 28 2 50S ribosomal protein L34 1299
16 1NWY 29 2 ribosomal protein L34 1299
17 1SM1 3 2 50S RIBOSOMAL PROTEIN L34 1299
18 2ZJQ 28 2 50S ribosomal protein L34 1299
19 1NWX 29 2 ribosomal protein L34 1299
20 1XBP 29 2 50S ribosomal protein L34 1299
21 2ZJP 2 2 50S RIBOSOMAL PROTEIN L34 1299
22 4V4P 31 A7 50S ribosomal protein L34 274
23 4V4R 53 B7 50S ribosomal protein L34 274
24 4V4S 53 B7 50S ribosomal protein L34 274
25 4V4T 52 B7 50S ribosomal protein L34 274
26 4V49 52 B2 50S ribosomal protein L34 562
27 4V4A 50 B2 50S ribosomal protein L34 562
28 4V4G 50 B4, D4, F4, H4, J4 50S ribosomal protein L34 562