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 % 94 115 224
95 % 94 115 311 Flexibility: Low
Max RMSD: 6.8, Avg RMSD: 1.7
PDBFlex
90 % 94 115 328
70 % 95 118 345
50 % 95 129 347
40 % 95 129 376
30 % 95 129 384
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 % 99 137 179
95 % 99 137 240 Flexibility: No
Max RMSD: 1.1, Avg RMSD: 0.5
PDBFlex
90 % 99 137 253
70 % 100 151 259
50 % 105 159 254
40 % 105 159 270
30 % 105 159 278
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 % 94 117 220
95 % 94 117 305 Flexibility: No
Max RMSD: 1.1, Avg RMSD: 0.5
PDBFlex
90 % 94 117 322
70 % 94 117 359
50 % 95 120 402
40 % 95 122 419
30 % 95 122 423
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 % 97 133 182
95 % 97 133 248 Flexibility: Low
Max RMSD: 2.0, Avg RMSD: 1.0
PDBFlex
90 % 97 133 259
70 % 97 133 289
50 % 98 136 316
40 % 98 136 330
30 % 98 136 341
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 27198
95 % 3 5 14018 Flexibility: Low
Max RMSD: 1.3, Avg RMSD: 0.9
PDBFlex
90 % 3 5 13748
70 % 3 5 12897
50 % 3 5 11497
40 % 3 5 10420
30 % 3 5 9033
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 % 93 116 222
95 % 94 117 302 Flexibility: Low
Max RMSD: 3.3, Avg RMSD: 1.2
PDBFlex
90 % 94 117 317
70 % 95 122 327
50 % 95 131 340
40 % 100 139 320
30 % 100 142 326
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 % 92 112 228
95 % 92 112 316 Flexibility: Low
Max RMSD: 1.0, Avg RMSD: 0.5
PDBFlex
90 % 92 112 335
70 % 92 112 373
50 % 92 114 424
40 % 92 114 461
30 % 92 114 458
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 61 551
95 % 48 61 762 Flexibility: Low
Max RMSD: 3.5, Avg RMSD: 0.7
PDBFlex
90 % 48 61 789
70 % 48 62 817
50 % 50 67 749
40 % 50 67 784
30 % 50 67 773
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 Structural variation in cluster
100 % 100 138 175
95 % 100 138 235 Flexibility: Low
Max RMSD: 2.1, Avg RMSD: 0.7
PDBFlex
90 % 100 138 247
70 % 101 141 274
50 % 101 143 297
40 % 101 152 297
30 % 101 152 308
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 % 97 132 185
95 % 97 132 251 Flexibility: Low
Max RMSD: 1.4, Avg RMSD: 0.6
PDBFlex
90 % 97 132 262
70 % 97 132 290
50 % 98 147 288
40 % 98 147 304
30 % 98 147 318
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
100 % 50 64 490
95 % 50 64 685
90 % 50 64 714
70 % 50 64 765
50 % 52 79 571
40 % 52 79 614
30 % 52 79 611
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 % 98 137 178
95 % 99 138 237 Flexibility: Low
Max RMSD: 1.9, Avg RMSD: 1.0
PDBFlex
90 % 99 138 249
70 % 99 138 281
50 % 100 141 306
40 % 100 141 318
30 % 100 153 305
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 % 93 116 223
95 % 93 116 310 Flexibility: Low
Max RMSD: 2.9, Avg RMSD: 1.0
PDBFlex
90 % 93 116 327
70 % 94 119 342
50 % 94 121 395
40 % 94 121 422
30 % 94 124 416

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.