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 3404
95 % 3 19 3705 Flexibility: Low
Max RMSD: 1.9, Avg RMSD: 1.2
PDBFlex
90 % 3 19 3765
70 % 3 19 3703
50 % 3 19 3492
40 % 3 19 3358
30 % 3 19 3162
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 2044
95 % 4 24 2343 Flexibility: Low
Max RMSD: 1.6, Avg RMSD: 0.8
PDBFlex
90 % 4 24 2410
70 % 113 251 84
50 % 142 428 38
40 % 238 646 24
30 % 238 646 40
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 2038
95 % 4 24 2337 Flexibility: Low
Max RMSD: 8.4, Avg RMSD: 2.9
PDBFlex
90 % 4 24 2403
70 % 4 24 2395
50 % 141 410 49
40 % 141 410 70
30 % 141 410 85
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 1754
95 % 4 27 2061 Flexibility: Low
Max RMSD: 5.2, Avg RMSD: 2.7
PDBFlex
90 % 4 27 2112
70 % 107 214 96
50 % 141 416 44
40 % 141 416 63
30 % 141 416 79
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 2064
95 % 4 24 2371 Flexibility: Low
Max RMSD: 1.7, Avg RMSD: 0.9
PDBFlex
90 % 4 24 2437
70 % 4 24 2450
50 % 142 412 39
40 % 142 412 55
30 % 142 414 73
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 2221
95 % 4 24 2370 Flexibility: Low
Max RMSD: 2.8, Avg RMSD: 1.6
PDBFlex
90 % 4 24 2436
70 % 4 24 2428
50 % 141 411 48
40 % 141 411 69
30 % 141 411 84
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 3379
95 % 3 19 3674 Flexibility: Medium
Max RMSD: 7.0, Avg RMSD: 3.0
PDBFlex
90 % 3 19 3735
70 % 3 19 3676
50 % 3 19 3556
40 % 3 19 3409
30 % 3 19 3143
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 1683
95 % 4 28 1966 Flexibility: Low
Max RMSD: 1.4, Avg RMSD: 0.8
PDBFlex
90 % 4 28 2012
70 % 4 28 2036
50 % 142 415 41
40 % 142 423 53
30 % 142 423 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 1711
95 % 4 28 2000 Flexibility: Medium
Max RMSD: 7.9, Avg RMSD: 3.7
PDBFlex
90 % 4 28 2048
70 % 4 28 2074
50 % 112 236 117
40 % 141 410 71
30 % 141 410 86
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 1710
95 % 4 30 1849 Flexibility: Low
Max RMSD: 2.5, Avg RMSD: 1.1
PDBFlex
90 % 4 30 1892
70 % 4 30 1914
50 % 4 30 1933
40 % 4 30 1916
30 % 4 30 1853
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 1791
95 % 4 26 2093 Flexibility: Low
Max RMSD: 2.0, Avg RMSD: 1.1
PDBFlex
90 % 4 26 2147
70 % 4 26 2159
50 % 112 245 114
40 % 208 496 40
30 % 208 496 59
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 1914
95 % 4 25 2244 Flexibility: Low
Max RMSD: 3.3, Avg RMSD: 1.6
PDBFlex
90 % 4 25 2304
70 % 4 25 2311
50 % 141 413 47
40 % 141 415 64
30 % 141 415 80
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 2324
95 % 3 25 2623 Flexibility: Low
Max RMSD: 6.5, Avg RMSD: 1.7
PDBFlex
90 % 3 25 2695
70 % 3 25 2689
50 % 3 25 2663
40 % 3 25 2616
30 % 3 25 2437
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 1615
95 % 4 29 1887 Flexibility: Medium
Max RMSD: 11.9, Avg RMSD: 5.0
PDBFlex
90 % 4 29 1934
70 % 34 196 168
50 % 143 413 45
40 % 143 413 65
30 % 143 413 81
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 1790
95 % 4 26 2092 Flexibility: Low
Max RMSD: 2.8, Avg RMSD: 1.5
PDBFlex
90 % 4 26 2146
70 % 4 26 2158
50 % 4 26 2167
40 % 4 26 2136
30 % 208 477 64
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 1948
95 % 4 24 2258 Flexibility: Low
Max RMSD: 1.8, Avg RMSD: 0.9
PDBFlex
90 % 4 24 2319
70 % 4 24 2325
50 % 38 221 196
40 % 142 416 59
30 % 142 416 75
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 4051
95 % 1 12 4420 Flexibility: No
Max RMSD: 0.5, Avg RMSD: 0.4
PDBFlex
90 % 1 12 4457
70 % 1 12 4358
50 % 103 253 120
40 % 104 271 134
30 % 104 272 145
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 1367
95 % 4 34 1604 Flexibility: Low
Max RMSD: 1.5, Avg RMSD: 0.9
PDBFlex
90 % 4 34 1627
70 % 4 34 1642
50 % 141 401 60
40 % 141 407 73
30 % 141 407 87
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 13243
95 % 1 6 13852 Flexibility: Low
Max RMSD: 0.5, Avg RMSD: 0.5
PDBFlex
90 % 1 6 12457
70 % 1 6 11754
50 % 1 6 10168
40 % 1 6 9184
30 % 1 6 7920
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 1707
95 % 4 28 1994 Flexibility: Low
Max RMSD: 1.8, Avg RMSD: 1.1
PDBFlex
90 % 4 28 2044
70 % 33 192 175
50 % 38 223 195
40 % 38 223 206
30 % 38 223 225
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 1987
95 % 4 24 2285 Flexibility: Low
Max RMSD: 7.5, Avg RMSD: 2.2
PDBFlex
90 % 4 24 2349
70 % 108 211 98
50 % 142 417 42
40 % 142 417 61
30 % 142 417 77
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 1708
95 % 4 28 1995 Flexibility: Low
Max RMSD: 3.7, Avg RMSD: 1.7
PDBFlex
90 % 4 28 2045
70 % 4 28 2069
50 % 108 215 130
40 % 142 405 78
30 % 142 405 89
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 2265
95 % 3 22 2560 Flexibility: Low
Max RMSD: 1.5, Avg RMSD: 1.0
PDBFlex
90 % 3 22 2630
70 % 100 350 50
50 % 100 353 86
40 % 100 353 101
30 % 100 353 116
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 1730
95 % 4 27 2054 Flexibility: Low
Max RMSD: 2.7, Avg RMSD: 1.5
PDBFlex
90 % 4 27 2104
70 % 4 27 2126
50 % 148 421 46
40 % 148 425 57
30 % 148 426 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 1629
95 % 4 29 1904 Flexibility: Low
Max RMSD: 2.2, Avg RMSD: 1.2
PDBFlex
90 % 4 29 1948
70 % 4 29 1968
50 % 108 216 129
40 % 143 417 60
30 % 143 417 76
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 2083
95 % 4 24 2351 Flexibility: Low
Max RMSD: 2.3, Avg RMSD: 1.4
PDBFlex
90 % 4 24 2418
70 % 110 213 94
50 % 148 415 43
40 % 148 415 62
30 % 148 415 78
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 46704
95 % 1 2 38916 Flexibility: Low
Max RMSD: 0.7, Avg RMSD: 0.7
PDBFlex
90 % 1 2 37096
70 % 1 2 32858
50 % 1 2 27963
40 % 1 2 24523
30 % 1 2 20443
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 17203
95 % 1 5 15957 Flexibility: No
Max RMSD: 0.6, Avg RMSD: 0.4
PDBFlex
90 % 1 5 15609
70 % 1 5 14533
50 % 91 158 174
40 % 118 326 103
30 % 118 329 117
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 2293
95 % 4 21 2595 Flexibility: Low
Max RMSD: 3.8, Avg RMSD: 2.1
PDBFlex
90 % 4 21 2666
70 % 20 65 571
50 % 50 254 156
40 % 50 257 164
30 % 50 260 182

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