Sequence Similarity Clusters for the Entities in PDB 1Y1W

Entity #1 | Chains: T
5'-D(P*AP*GP*TP*AP*CP*TP*TP*AP*CP*GP*CP*CP*TP*GP*GP*TP*CP*AP*T)-3' dna, length: 19 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
Entity #10 | Chains: G
DNA-directed RNA polymerase II 19 kDa polypeptide protein, length: 171 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name Structural variation in cluster
100 % 45 64 525
95 % 45 64 717 Flexibility: Low
Max RMSD: 4.4, Avg RMSD: 0.8
PDBFlex
90 % 45 64 747
70 % 45 64 798
50 % 47 82 570
40 % 47 82 607
30 % 47 82 597
Entity #11 | Chains: H
DNA-directed RNA polymerases I, II, and III 14.5 kDa polypeptide protein, length: 146 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name Structural variation in cluster
100 % 88 142 175
95 % 89 143 234 Flexibility: Low
Max RMSD: 1.9, Avg RMSD: 0.9
PDBFlex
90 % 89 143 249
70 % 89 143 281
50 % 90 148 299
40 % 90 148 314
30 % 90 161 292
Entity #12 | Chains: I
DNA-directed RNA polymerase II subunit 9 protein, length: 122 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name Structural variation in cluster
100 % 85 116 228
95 % 85 116 321 Flexibility: Low
Max RMSD: 2.7, Avg RMSD: 0.9
PDBFlex
90 % 85 116 340
70 % 86 121 356
50 % 86 123 407
40 % 86 123 437
30 % 86 126 427
Entity #13 | Chains: J
DNA-directed RNA polymerases I/II/III subunit 10 protein, length: 70 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name Structural variation in cluster
100 % 89 142 176
95 % 89 142 236 Flexibility: No
Max RMSD: 1.1, Avg RMSD: 0.5
PDBFlex
90 % 89 142 250
70 % 90 159 251
50 % 95 167 247
40 % 95 167 266
30 % 95 167 272
Entity #14 | Chains: K
DNA-directed RNA polymerase II 13.6 kDa polypeptide protein, length: 120 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name Structural variation in cluster
100 % 85 117 224
95 % 85 117 316 Flexibility: No
Max RMSD: 1.1, Avg RMSD: 0.5
PDBFlex
90 % 85 117 334
70 % 85 117 370
50 % 86 122 416
40 % 86 124 435
30 % 86 124 436
Entity #15 | Chains: L
DNA-directed RNA polymerases I, II, and III 7.7 kDa polypeptide protein, length: 70 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name Structural variation in cluster
100 % 87 138 185
95 % 87 138 245 Flexibility: Low
Max RMSD: 2.0, Avg RMSD: 1.0
PDBFlex
90 % 87 138 260
70 % 87 138 290
50 % 88 143 313
40 % 88 143 331
30 % 88 143 338
Entity #2 | Chains: N
5'-D(*AP*AP*GP*TP*AP*CP*T)-3' dna, length: 7 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
Entity #3 | Chains: P
5'-R(*AP*AP*GP*AP*CP*CP*AP*GP*GP*C)-3' rna, length: 10 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
Entity #4 | Chains: A
DNA-directed RNA polymerase II largest subunit protein, length: 1733 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name Structural variation in cluster
100 % 85 115 230
95 % 85 115 322 Flexibility: Low
Max RMSD: 6.8, Avg RMSD: 1.6
PDBFlex
90 % 85 115 341
70 % 86 120 357
50 % 86 132 369
40 % 86 132 394
30 % 86 132 399
Entity #5 | Chains: B
DNA-directed RNA polymerase II 140 kDa polypeptide protein, length: 1224 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name Structural variation in cluster
100 % 84 116 226
95 % 85 117 314 Flexibility: Low
Max RMSD: 3.3, Avg RMSD: 1.3
PDBFlex
90 % 85 117 331
70 % 86 124 342
50 % 86 134 357
40 % 91 142 327
30 % 91 145 331
Entity #6 | Chains: C
DNA-directed RNA polymerase II 45 kDa polypeptide protein, length: 318 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name Structural variation in cluster
100 % 83 112 233
95 % 83 112 328 Flexibility: Low
Max RMSD: 1.0, Avg RMSD: 0.5
PDBFlex
90 % 83 112 347
70 % 83 112 380
50 % 83 114 441
40 % 83 114 473
30 % 83 114 472
Entity #7 | Chains: D
DNA-directed RNA polymerase II 32 kDa polypeptide protein, length: 221 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name Structural variation in cluster
100 % 43 61 566
95 % 43 61 782 Flexibility: Low
Max RMSD: 3.5, Avg RMSD: 0.8
PDBFlex
90 % 43 61 810
70 % 43 62 835
50 % 45 69 754
40 % 45 69 787
30 % 45 69 780
Entity #8 | Chains: E
DNA-directed RNA polymerases I, II, and III 27 kDa polypeptide protein, length: 215 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name Structural variation in cluster
100 % 90 143 173
95 % 90 143 233 Flexibility: Low
Max RMSD: 2.1, Avg RMSD: 0.7
PDBFlex
90 % 90 143 248
70 % 91 148 272
50 % 91 150 291
40 % 91 160 286
30 % 91 160 293
Entity #9 | Chains: F
DNA-directed RNA polymerases 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 % 87 137 188
95 % 87 137 248 Flexibility: Low
Max RMSD: 1.4, Avg RMSD: 0.6
PDBFlex
90 % 87 137 263
70 % 87 137 294
50 % 88 155 279
40 % 88 155 298
30 % 88 155 309

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.