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 Structural variation in cluster
100 % 109 176 170
95 % 110 177 225 Flexibility: Low
Max RMSD: 1.9, Avg RMSD: 1.0
PDBFlex
90 % 110 177 237
70 % 110 177 260
50 % 112 196 247
40 % 112 196 260
30 % 112 210 253
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 % 104 132 228
95 % 104 132 312 Flexibility: Low
Max RMSD: 2.9, Avg RMSD: 1.0
PDBFlex
90 % 104 132 325
70 % 106 151 323
50 % 107 153 377
40 % 107 153 398
30 % 107 168 376
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 Structural variation in cluster
100 % 110 176 171
95 % 110 176 226 Flexibility: No
Max RMSD: 1.1, Avg RMSD: 0.5
PDBFlex
90 % 110 176 239
70 % 113 210 197
50 % 113 210 220
40 % 113 210 241
30 % 113 210 252
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 % 105 133 226
95 % 105 133 309 Flexibility: No
Max RMSD: 1.1, Avg RMSD: 0.5
PDBFlex
90 % 105 133 322
70 % 105 133 364
50 % 107 152 382
40 % 108 154 397
30 % 108 154 409
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 % 108 172 177
95 % 108 172 233 Flexibility: Low
Max RMSD: 2.0, Avg RMSD: 1.0
PDBFlex
90 % 108 172 244
70 % 108 172 273
50 % 110 191 255
40 % 110 191 271
30 % 110 191 285
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 31523
95 % 4 5 17261 Flexibility: Low
Max RMSD: 2.8, Avg RMSD: 1.9
PDBFlex
90 % 4 5 15800
70 % 4 5 14851
50 % 4 6 11382
40 % 4 6 10680
30 % 4 6 9813
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 % 105 131 233
95 % 105 131 317 Flexibility: Low
Max RMSD: 6.8, Avg RMSD: 1.6
PDBFlex
90 % 105 131 326
70 % 107 150 325
50 % 108 152 381
40 % 108 152 401
30 % 108 152 412
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 % 104 132 231
95 % 105 133 310 Flexibility: Low
Max RMSD: 3.3, Avg RMSD: 1.2
PDBFlex
90 % 105 133 323
70 % 108 154 316
50 % 108 167 346
40 % 113 175 317
30 % 113 190 287
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 % 103 128 239
95 % 103 128 326 Flexibility: Low
Max RMSD: 1.0, Avg RMSD: 0.5
PDBFlex
90 % 103 128 335
70 % 103 128 385
50 % 103 128 450
40 % 104 130 465
30 % 104 130 489
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 % 51 70 555
95 % 51 70 748 Flexibility: Low
Max RMSD: 3.5, Avg RMSD: 0.8
PDBFlex
90 % 51 70 771
70 % 51 71 803
50 % 51 71 858
40 % 51 71 905
30 % 51 71 941
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 % 111 177 169
95 % 111 177 224 Flexibility: Low
Max RMSD: 2.1, Avg RMSD: 0.7
PDBFlex
90 % 111 177 236
70 % 113 196 235
50 % 114 198 241
40 % 114 211 239
30 % 114 211 250
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 % 108 171 179
95 % 108 171 235 Flexibility: Low
Max RMSD: 1.4, Avg RMSD: 0.6
PDBFlex
90 % 108 171 246
70 % 108 171 277
50 % 111 192 252
40 % 111 192 266
30 % 111 192 281
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 % 53 73 507
95 % 53 73 705 Flexibility: Low
Max RMSD: 4.4, Avg RMSD: 0.7
PDBFlex
90 % 53 73 736
70 % 53 73 772
50 % 57 108 488
40 % 57 108 525
30 % 57 108 545

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