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 % 100 124 228
95 % 100 124 317 Flexibility: Low
Max RMSD: 5.3, Avg RMSD: 1.6
PDBFlex
90 % 100 124 330
70 % 102 129 355
50 % 102 142 377
40 % 102 142 395
30 % 102 142 399
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 % 105 159 174
95 % 105 159 235 Flexibility: No
Max RMSD: 1.1, Avg RMSD: 0.5
PDBFlex
90 % 105 159 247
70 % 107 177 236
50 % 112 185 230
40 % 112 185 249
30 % 112 185 259
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 % 100 126 220
95 % 100 126 313 Flexibility: No
Max RMSD: 1.0, Avg RMSD: 0.5
PDBFlex
90 % 100 126 325
70 % 100 126 373
50 % 102 131 416
40 % 102 133 426
30 % 102 133 426
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 % 103 155 176
95 % 103 155 240 Flexibility: Low
Max RMSD: 2.0, Avg RMSD: 1.0
PDBFlex
90 % 103 155 252
70 % 103 155 284
50 % 105 160 291
40 % 105 160 313
30 % 105 160 319
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 29331
95 % 3 5 15108 Flexibility: Low
Max RMSD: 2.8, Avg RMSD: 1.9
PDBFlex
90 % 3 5 14822
70 % 3 5 13891
50 % 3 6 10786
40 % 3 6 9767
30 % 3 6 8516
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 % 99 125 223
95 % 100 126 309 Flexibility: Low
Max RMSD: 3.3, Avg RMSD: 1.3
PDBFlex
90 % 100 126 321
70 % 102 133 336
50 % 102 144 372
40 % 107 152 338
30 % 107 163 306
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 % 98 121 235
95 % 98 121 324 Flexibility: Low
Max RMSD: 1.0, Avg RMSD: 0.5
PDBFlex
90 % 98 121 340
70 % 98 121 382
50 % 98 123 439
40 % 98 123 464
30 % 98 123 460
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 % 49 65 554
95 % 49 65 751 Flexibility: Low
Max RMSD: 3.5, Avg RMSD: 0.7
PDBFlex
90 % 49 65 780
70 % 49 66 806
50 % 52 73 746
40 % 52 73 778
30 % 52 73 776
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 % 106 160 171
95 % 106 160 230 Flexibility: Low
Max RMSD: 2.1, Avg RMSD: 0.7
PDBFlex
90 % 106 160 241
70 % 108 165 257
50 % 108 167 273
40 % 108 178 266
30 % 108 178 280
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 % 103 154 177
95 % 103 154 241 Flexibility: Low
Max RMSD: 1.4, Avg RMSD: 0.6
PDBFlex
90 % 103 154 253
70 % 103 154 285
50 % 105 173 262
40 % 105 173 273
30 % 105 173 286
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 % 51 68 500
95 % 51 68 686 Flexibility: Low
Max RMSD: 4.2, Avg RMSD: 0.7
PDBFlex
90 % 51 68 715
70 % 51 68 760
50 % 54 87 562
40 % 54 87 599
30 % 54 87 591
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 % 104 159 173
95 % 105 160 232 Flexibility: Low
Max RMSD: 1.9, Avg RMSD: 1.0
PDBFlex
90 % 105 160 243
70 % 105 160 272
50 % 107 165 283
40 % 107 165 299
30 % 107 179 278
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 % 99 125 227
95 % 99 125 316 Flexibility: Low
Max RMSD: 2.9, Avg RMSD: 1.0
PDBFlex
90 % 99 125 329
70 % 101 130 354
50 % 101 132 410
40 % 101 132 430
30 % 101 143 397

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