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 % 111 132 258
95 % 111 132 345 Flexibility: Low
Max RMSD: 6.8, Avg RMSD: 1.6
PDBFlex
90 % 111 132 358
70 % 113 151 341
50 % 114 153 399
40 % 114 153 423
30 % 114 153 438
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 % 116 177 183
95 % 116 177 241 Flexibility: No
Max RMSD: 1.1, Avg RMSD: 0.5
PDBFlex
90 % 116 177 251
70 % 119 213 237
50 % 119 213 248
40 % 119 213 264
30 % 119 213 281
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 % 111 134 242
95 % 111 134 331 Flexibility: No
Max RMSD: 1.1, Avg RMSD: 0.5
PDBFlex
90 % 111 134 343
70 % 111 134 384
50 % 113 153 404
40 % 114 155 418
30 % 114 155 433
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 % 114 173 187
95 % 114 173 244 Flexibility: Low
Max RMSD: 2.0, Avg RMSD: 1.0
PDBFlex
90 % 114 173 256
70 % 114 173 296
50 % 116 192 312
40 % 116 192 329
30 % 116 192 345
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 % 110 133 249
95 % 111 134 329 Flexibility: Low
Max RMSD: 3.3, Avg RMSD: 1.2
PDBFlex
90 % 111 134 345
70 % 114 155 333
50 % 114 170 362
40 % 122 178 355
30 % 122 193 337
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 % 109 129 269
95 % 109 129 360 Flexibility: Low
Max RMSD: 1.0, Avg RMSD: 0.5
PDBFlex
90 % 109 129 375
70 % 109 129 413
50 % 109 129 462
40 % 110 131 484
30 % 110 131 515
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 % 117 178 181
95 % 117 178 239 Flexibility: Low
Max RMSD: 2.1, Avg RMSD: 0.7
PDBFlex
90 % 117 178 248
70 % 119 197 259
50 % 120 199 287
40 % 120 214 256
30 % 120 214 272
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 Structural variation in cluster
100 % 114 172 188
95 % 114 172 245 Flexibility: Low
Max RMSD: 1.4, Avg RMSD: 0.6
PDBFlex
90 % 114 172 257
70 % 114 172 298
50 % 117 193 305
40 % 117 193 322
30 % 117 193 335
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 % 115 177 182
95 % 116 178 238 Flexibility: Low
Max RMSD: 1.9, Avg RMSD: 1.0
PDBFlex
90 % 116 178 247
70 % 116 178 285
50 % 118 197 298
40 % 118 197 312
30 % 118 213 287
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 % 110 133 250
95 % 110 133 336 Flexibility: Low
Max RMSD: 2.9, Avg RMSD: 1.0
PDBFlex
90 % 110 133 352
70 % 112 152 339
50 % 113 154 395
40 % 113 154 420
30 % 113 169 397

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