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 % 94 115 226
95 % 94 115 318 Flexibility: Low
Max RMSD: 6.8, Avg RMSD: 1.6
PDBFlex
90 % 94 115 335
70 % 96 120 352
50 % 96 131 363
40 % 96 131 387
30 % 96 131 395
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
100 % 99 142 173
95 % 99 142 233
90 % 99 142 248
70 % 101 158 251
50 % 106 166 247
40 % 106 166 264
30 % 106 166 271
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 % 94 117 221
95 % 94 117 311 Flexibility: No
Max RMSD: 1.1, Avg RMSD: 0.5
PDBFlex
90 % 94 117 328
70 % 94 117 365
50 % 96 122 410
40 % 96 124 426
30 % 96 124 427
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 % 97 138 180
95 % 97 138 242 Flexibility: Low
Max RMSD: 2.0, Avg RMSD: 1.0
PDBFlex
90 % 97 138 256
70 % 97 138 286
50 % 99 143 309
40 % 99 143 321
30 % 99 143 334
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 27589
95 % 3 5 14223 Flexibility: Low
Max RMSD: 1.3, Avg RMSD: 0.9
PDBFlex
90 % 3 5 13946
70 % 3 5 13084
50 % 3 6 10168
40 % 3 6 9217
30 % 3 6 8030
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 % 93 116 223
95 % 94 117 308 Flexibility: Low
Max RMSD: 3.3, Avg RMSD: 1.3
PDBFlex
90 % 94 117 324
70 % 96 124 332
50 % 96 133 349
40 % 101 141 322
30 % 101 144 328
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 % 92 112 230
95 % 92 112 322 Flexibility: Low
Max RMSD: 1.0, Avg RMSD: 0.5
PDBFlex
90 % 92 112 341
70 % 92 112 376
50 % 92 114 437
40 % 92 114 465
30 % 92 114 467
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 61 562
95 % 48 61 780 Flexibility: Low
Max RMSD: 3.5, Avg RMSD: 0.7
PDBFlex
90 % 48 61 808
70 % 48 62 832
50 % 51 69 749
40 % 51 69 778
30 % 51 69 773
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
100 % 100 143 170
95 % 100 143 231
90 % 100 143 246
70 % 102 148 268
50 % 102 150 289
40 % 102 159 285
30 % 102 159 293
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 % 97 137 183
95 % 97 137 245 Flexibility: Low
Max RMSD: 1.4, Avg RMSD: 0.6
PDBFlex
90 % 97 137 259
70 % 97 137 290
50 % 99 154 281
40 % 99 154 297
30 % 99 154 308
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 64 514
95 % 50 64 706 Flexibility: Low
Max RMSD: 4.4, Avg RMSD: 0.6
PDBFlex
90 % 50 64 735
70 % 50 64 788
50 % 53 81 569
40 % 53 81 609
30 % 53 81 604
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 % 98 142 172
95 % 99 143 232 Flexibility: Low
Max RMSD: 1.9, Avg RMSD: 0.9
PDBFlex
90 % 99 143 247
70 % 99 143 277
50 % 101 148 293
40 % 101 148 307
30 % 101 160 292
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 % 93 116 225
95 % 93 116 317 Flexibility: Low
Max RMSD: 2.9, Avg RMSD: 1.0
PDBFlex
90 % 93 116 334
70 % 95 121 351
50 % 95 123 402
40 % 95 123 431
30 % 95 126 420

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.