Sequence Similarity Clusters for the Entities in PDB 1NIK

Entity #1 | Chains: A
RPB1 protein, length: 1733 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name Structural variation in cluster
100 % 104 118 235
95 % 104 118 323 Flexibility: Low
Max RMSD: 5.3, Avg RMSD: 1.6
PDBFlex
90 % 104 118 341
70 % 106 123 367
50 % 107 135 384
40 % 107 135 414
30 % 107 135 413
Entity #10 | Chains: J
DNA-directed RNA polymerase II, chain RPB10 protein, length: 70 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name Structural variation in cluster
100 % 109 153 176
95 % 109 153 238 Flexibility: No
Max RMSD: 1.1, Avg RMSD: 0.5
PDBFlex
90 % 109 153 250
70 % 112 170 246
50 % 120 178 235
40 % 120 178 254
30 % 120 178 263
Entity #11 | Chains: K
DNA-directed RNA polymerase II, chain RPB11 protein, length: 120 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name Structural variation in cluster
100 % 104 120 230
95 % 104 120 319 Flexibility: No
Max RMSD: 1.0, Avg RMSD: 0.5
PDBFlex
90 % 104 120 336
70 % 104 120 378
50 % 106 125 427
40 % 107 127 441
30 % 107 127 444
Entity #12 | Chains: L
DNA-directed RNA polymerase II, chain RPB12 protein, length: 70 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name Structural variation in cluster
100 % 107 149 181
95 % 107 149 241 Flexibility: Low
Max RMSD: 2.0, Avg RMSD: 1.0
PDBFlex
90 % 107 149 254
70 % 107 149 289
50 % 109 154 304
40 % 109 154 322
30 % 109 154 326
Entity #2 | Chains: B
ORF YOR151c protein, length: 1224 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name Structural variation in cluster
100 % 103 119 231
95 % 104 120 318 Flexibility: Low
Max RMSD: 3.3, Avg RMSD: 1.3
PDBFlex
90 % 104 120 334
70 % 107 127 348
50 % 107 137 376
40 % 115 145 347
30 % 115 156 315
Entity #3 | Chains: C
DNA-directed RNA polymerase II, chain RPB3 protein, length: 318 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name Structural variation in cluster
100 % 102 115 237
95 % 102 115 332 Flexibility: Low
Max RMSD: 1.0, Avg RMSD: 0.5
PDBFlex
90 % 102 115 352
70 % 102 115 388
50 % 103 117 448
40 % 103 117 478
30 % 103 117 471
Entity #4 | Chains: D
DNA-directed RNA polymerase II, chain RPB4 protein, length: 161 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
Entity #5 | Chains: E
DNA-directed RNA polymerase II, chain RPB5 protein, length: 215 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name Structural variation in cluster
100 % 110 154 172
95 % 110 154 233 Flexibility: Low
Max RMSD: 2.1, Avg RMSD: 0.7
PDBFlex
90 % 110 154 245
70 % 112 159 267
50 % 113 161 282
40 % 113 171 274
30 % 113 171 283
Entity #6 | Chains: F
DNA-directed RNA polymerase I, II and III 23 kDa polypeptide protein, length: 155 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 107 148 182
95 % 107 148 243
90 % 107 148 256
70 % 107 148 291
50 % 110 166 273
40 % 110 166 287
30 % 110 166 297
Entity #7 | Chains: G
DNA-directed RNA polymerase II, chain RPB7 protein, length: 170 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
Entity #8 | Chains: H
DNA-directed RNA polymerase subunit RPB8 protein, length: 146 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name Structural variation in cluster
100 % 108 153 175
95 % 109 154 234 Flexibility: Low
Max RMSD: 1.9, Avg RMSD: 1.0
PDBFlex
90 % 109 154 246
70 % 109 154 280
50 % 111 159 287
40 % 111 159 307
30 % 112 172 281
Entity #9 | Chains: I
DNA-directed RNA polymerase II, chain RPB9 protein, length: 122 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name Structural variation in cluster
100 % 103 119 234
95 % 103 119 321 Flexibility: Low
Max RMSD: 2.9, Avg RMSD: 1.0
PDBFlex
90 % 103 119 339
70 % 105 124 366
50 % 106 126 418
40 % 106 126 446
30 % 106 137 405

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