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 % 111 127 236
95 % 111 127 312 Flexibility: Low
Max RMSD: 6.8, Avg RMSD: 1.6
PDBFlex
90 % 111 127 324
70 % 113 132 347
50 % 114 145 379
40 % 114 145 407
30 % 114 145 405
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 % 116 162 183
95 % 116 162 233 Flexibility: No
Max RMSD: 1.1, Avg RMSD: 0.5
PDBFlex
90 % 116 162 241
70 % 119 180 230
50 % 127 188 229
40 % 127 188 254
30 % 127 188 274
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 % 111 129 232
95 % 111 129 300 Flexibility: No
Max RMSD: 1.1, Avg RMSD: 0.5
PDBFlex
90 % 111 129 312
70 % 111 129 361
50 % 113 134 407
40 % 114 136 425
30 % 114 136 426
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 % 114 158 185
95 % 114 158 241 Flexibility: Low
Max RMSD: 2.0, Avg RMSD: 1.0
PDBFlex
90 % 114 158 247
70 % 114 158 278
50 % 116 163 296
40 % 116 163 327
30 % 116 163 334
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 % 111 129 233
95 % 111 129 306 Flexibility: Low
Max RMSD: 3.3, Avg RMSD: 1.2
PDBFlex
90 % 111 129 317
70 % 114 136 335
50 % 114 147 373
40 % 122 155 353
30 % 234 308 143
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 % 109 124 244
95 % 109 124 321 Flexibility: Low
Max RMSD: 1.0, Avg RMSD: 0.5
PDBFlex
90 % 109 124 332
70 % 109 124 376
50 % 109 124 444
40 % 109 124 475
30 % 109 124 480
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 % 117 163 182
95 % 117 163 232 Flexibility: Low
Max RMSD: 2.1, Avg RMSD: 0.7
PDBFlex
90 % 117 163 238
70 % 119 168 254
50 % 120 170 271
40 % 120 181 278
30 % 120 181 294
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 % 114 157 186
95 % 114 157 242 Flexibility: Low
Max RMSD: 1.4, Avg RMSD: 0.6
PDBFlex
90 % 114 157 248
70 % 114 157 281
50 % 117 176 262
40 % 117 176 288
30 % 117 176 298
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 % 115 162 184
95 % 116 163 231 Flexibility: Low
Max RMSD: 1.9, Avg RMSD: 0.9
PDBFlex
90 % 116 163 240
70 % 116 163 271
50 % 118 168 282
40 % 118 168 314
30 % 119 182 288
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 % 110 128 234
95 % 110 128 307 Flexibility: Low
Max RMSD: 2.9, Avg RMSD: 1.0
PDBFlex
90 % 110 128 318
70 % 112 133 343
50 % 113 135 404
40 % 113 135 428
30 % 113 146 404

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