Sequence Similarity Clusters for the Entities in PDB 1Y1V

Entity #1 | 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 % 94 115 230
95 % 94 115 322 Flexibility: Low
Max RMSD: 6.8, Avg RMSD: 1.6
PDBFlex
90 % 94 115 341
70 % 96 120 357
50 % 96 132 369
40 % 96 132 394
30 % 96 132 399
Entity #10 | 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 % 99 142 176
95 % 99 142 236 Flexibility: No
Max RMSD: 1.1, Avg RMSD: 0.5
PDBFlex
90 % 99 142 250
70 % 101 159 251
50 % 106 167 247
40 % 106 167 266
30 % 106 167 272
Entity #11 | 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 % 94 117 224
95 % 94 117 316 Flexibility: No
Max RMSD: 1.1, Avg RMSD: 0.5
PDBFlex
90 % 94 117 334
70 % 94 117 370
50 % 96 122 416
40 % 96 124 435
30 % 96 124 436
Entity #12 | 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 % 97 138 185
95 % 97 138 245 Flexibility: Low
Max RMSD: 2.0, Avg RMSD: 1.0
PDBFlex
90 % 97 138 260
70 % 97 138 290
50 % 99 143 313
40 % 99 143 331
30 % 99 143 338
Entity #13 | Chains: S
Transcription elongation factor S-II protein, length: 179 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name Structural variation in cluster
100 % 1 3 28087
95 % 3 5 14454 Flexibility: Low
Max RMSD: 2.8, Avg RMSD: 2.3
PDBFlex
90 % 3 5 14181
70 % 3 5 13321
50 % 3 6 10350
40 % 3 6 9386
30 % 3 6 8181
Entity #2 | 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 % 93 116 226
95 % 94 117 314 Flexibility: Low
Max RMSD: 3.3, Avg RMSD: 1.3
PDBFlex
90 % 94 117 331
70 % 96 124 342
50 % 96 134 357
40 % 101 142 327
30 % 101 145 331
Entity #3 | 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 % 92 112 233
95 % 92 112 328 Flexibility: Low
Max RMSD: 1.0, Avg RMSD: 0.5
PDBFlex
90 % 92 112 347
70 % 92 112 380
50 % 92 114 441
40 % 92 114 473
30 % 92 114 472
Entity #4 | 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 % 48 61 566
95 % 48 61 782 Flexibility: Low
Max RMSD: 3.5, Avg RMSD: 0.8
PDBFlex
90 % 48 61 810
70 % 48 62 835
50 % 51 69 754
40 % 51 69 787
30 % 51 69 780
Entity #5 | 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 % 100 143 173
95 % 100 143 233 Flexibility: Low
Max RMSD: 2.1, Avg RMSD: 0.7
PDBFlex
90 % 100 143 248
70 % 102 148 272
50 % 102 150 291
40 % 102 160 286
30 % 102 160 293
Entity #6 | 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 % 97 137 188
95 % 97 137 248 Flexibility: Low
Max RMSD: 1.4, Avg RMSD: 0.6
PDBFlex
90 % 97 137 263
70 % 97 137 294
50 % 99 155 279
40 % 99 155 298
30 % 99 155 309
Entity #7 | 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 % 50 64 525
95 % 50 64 717 Flexibility: Low
Max RMSD: 4.4, Avg RMSD: 0.8
PDBFlex
90 % 50 64 747
70 % 50 64 798
50 % 53 82 570
40 % 53 82 607
30 % 53 82 597
Entity #8 | 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 % 98 142 175
95 % 99 143 234 Flexibility: Low
Max RMSD: 1.9, Avg RMSD: 0.9
PDBFlex
90 % 99 143 249
70 % 99 143 281
50 % 101 148 299
40 % 101 148 314
30 % 101 161 292
Entity #9 | 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 % 93 116 228
95 % 93 116 321 Flexibility: Low
Max RMSD: 2.7, Avg RMSD: 0.9
PDBFlex
90 % 93 116 340
70 % 95 121 356
50 % 95 123 407
40 % 95 123 437
30 % 95 126 427

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.