Sequence Similarity Clusters for the Entities in PDB 1Y1Y

Entity #1 | Chains: T
5'-D(P*TP*AP*CP*GP*CP*CP*T)-3' dna, length: 7 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
Entity #10 | 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
100 % 101 137 179
95 % 102 138 238
90 % 102 138 252
70 % 102 138 283
50 % 103 141 307
40 % 103 141 320
30 % 104 153 306
Entity #11 | 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 % 96 116 225
95 % 96 116 316 Flexibility: Low
Max RMSD: 2.9, Avg RMSD: 1.0
PDBFlex
90 % 96 116 332
70 % 97 119 348
50 % 98 121 400
40 % 98 121 425
30 % 98 124 420
Entity #12 | 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 % 102 137 180
95 % 102 137 241
90 % 102 137 255
70 % 104 151 262
50 % 109 159 256
40 % 109 159 272
30 % 109 159 280
Entity #13 | 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 % 97 117 221
95 % 97 117 310 Flexibility: No
Max RMSD: 1.1, Avg RMSD: 0.5
PDBFlex
90 % 97 117 326
70 % 97 117 364
50 % 98 120 407
40 % 99 122 423
30 % 99 122 426
Entity #14 | 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 % 100 133 183
95 % 100 133 249 Flexibility: Low
Max RMSD: 2.0, Avg RMSD: 1.0
PDBFlex
90 % 100 133 261
70 % 100 133 294
50 % 101 136 318
40 % 101 136 334
30 % 101 136 345
Entity #15 | 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 % 2 3 27262
95 % 4 5 14053 Flexibility: Low
Max RMSD: 1.3, Avg RMSD: 0.9
PDBFlex
90 % 4 5 13779
70 % 4 5 12934
50 % 4 5 11523
40 % 4 5 10447
30 % 4 5 9060
Entity #2 | Chains: P
5'-R(P*AP*GP*GP*C)-3' rna, length: 4 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
Entity #3 | 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 % 97 115 226
95 % 97 115 317 Flexibility: Low
Max RMSD: 6.8, Avg RMSD: 1.7
PDBFlex
90 % 97 115 333
70 % 98 118 350
50 % 99 129 355
40 % 99 129 386
30 % 99 129 391
Entity #4 | 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 % 96 116 223
95 % 97 117 307 Flexibility: Low
Max RMSD: 3.3, Avg RMSD: 1.2
PDBFlex
90 % 97 117 322
70 % 99 122 332
50 % 99 131 343
40 % 104 139 322
30 % 104 142 328
Entity #5 | 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 % 95 112 230
95 % 95 112 322 Flexibility: Low
Max RMSD: 1.0, Avg RMSD: 0.5
PDBFlex
90 % 95 112 340
70 % 95 112 376
50 % 96 114 433
40 % 96 114 464
30 % 96 114 460
Entity #6 | 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 % 50 61 556
95 % 50 61 768 Flexibility: Low
Max RMSD: 3.5, Avg RMSD: 0.7
PDBFlex
90 % 50 61 794
70 % 50 62 822
50 % 52 67 752
40 % 52 67 788
30 % 52 67 776
Entity #7 | 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 % 103 138 176
95 % 103 138 237 Flexibility: Low
Max RMSD: 2.1, Avg RMSD: 0.7
PDBFlex
90 % 103 138 251
70 % 104 141 276
50 % 105 143 298
40 % 105 152 299
30 % 105 152 309
Entity #8 | 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 % 100 132 186
95 % 100 132 253 Flexibility: Low
Max RMSD: 1.4, Avg RMSD: 0.6
PDBFlex
90 % 100 132 265
70 % 100 132 295
50 % 102 147 290
40 % 102 147 306
30 % 102 147 320
Entity #9 | 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 % 52 64 495
95 % 52 64 690 Flexibility: Low
Max RMSD: 4.4, Avg RMSD: 0.8
PDBFlex
90 % 52 64 719
70 % 52 64 771
50 % 55 79 574
40 % 55 79 616
30 % 55 79 611

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.