Sequence Similarity Clusters for the Entities in PDB 1Y1W

Entity #1 | Chains: T
5'-D(P*AP*GP*TP*AP*CP*TP*TP*AP*CP*GP*CP*CP*TP*GP*GP*TP*CP*AP*T)-3' dna, length: 19 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
Entity #10 | 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 % 46 73 516
95 % 46 73 706 Flexibility: Low
Max RMSD: 4.4, Avg RMSD: 0.7
PDBFlex
90 % 46 73 735
70 % 46 73 774
50 % 48 108 489
40 % 48 108 522
30 % 48 108 547
Entity #11 | 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 % 96 176 170
95 % 97 177 225 Flexibility: Low
Max RMSD: 1.9, Avg RMSD: 1.0
PDBFlex
90 % 97 177 238
70 % 97 177 261
50 % 98 196 247
40 % 98 196 256
30 % 98 210 252
Entity #12 | 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 % 93 132 231
95 % 93 132 314 Flexibility: Low
Max RMSD: 2.9, Avg RMSD: 1.0
PDBFlex
90 % 93 132 323
70 % 94 151 323
50 % 94 153 380
40 % 94 153 395
30 % 94 168 375
Entity #13 | 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 % 97 176 171
95 % 97 176 228 Flexibility: No
Max RMSD: 1.1, Avg RMSD: 0.5
PDBFlex
90 % 97 176 240
70 % 98 210 198
50 % 98 210 219
40 % 98 210 237
30 % 98 210 251
Entity #14 | 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 % 93 133 226
95 % 93 133 310 Flexibility: No
Max RMSD: 1.1, Avg RMSD: 0.5
PDBFlex
90 % 93 133 320
70 % 93 133 364
50 % 94 152 385
40 % 94 154 392
30 % 94 154 404
Entity #15 | 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 % 95 172 175
95 % 95 172 234 Flexibility: Low
Max RMSD: 2.0, Avg RMSD: 1.0
PDBFlex
90 % 95 172 245
70 % 95 172 274
50 % 96 191 255
40 % 96 191 267
30 % 96 191 283
Entity #2 | Chains: N
5'-D(*AP*AP*GP*TP*AP*CP*T)-3' dna, length: 7 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
Entity #3 | Chains: P
5'-R(*AP*AP*GP*AP*CP*CP*AP*GP*GP*C)-3' rna, length: 10 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
Entity #4 | 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 % 93 131 232
95 % 93 131 316 Flexibility: Low
Max RMSD: 6.8, Avg RMSD: 1.6
PDBFlex
90 % 93 131 325
70 % 94 150 325
50 % 94 152 383
40 % 94 152 396
30 % 94 152 409
Entity #5 | 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 % 92 132 229
95 % 93 133 309 Flexibility: Low
Max RMSD: 3.3, Avg RMSD: 1.2
PDBFlex
90 % 93 133 319
70 % 94 154 316
50 % 94 167 347
40 % 99 175 315
30 % 99 190 286
Entity #6 | 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 % 91 128 238
95 % 91 128 329 Flexibility: Low
Max RMSD: 1.0, Avg RMSD: 0.5
PDBFlex
90 % 91 128 336
70 % 91 128 385
50 % 91 128 453
40 % 91 130 463
30 % 91 130 496
Entity #7 | 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 % 44 70 555
95 % 44 70 741 Flexibility: Low
Max RMSD: 3.5, Avg RMSD: 0.8
PDBFlex
90 % 44 70 777
70 % 44 71 806
50 % 44 71 861
40 % 44 71 902
30 % 44 71 946
Entity #8 | 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 % 98 177 169
95 % 98 177 226 Flexibility: Low
Max RMSD: 2.1, Avg RMSD: 0.7
PDBFlex
90 % 98 177 239
70 % 99 196 236
50 % 99 198 241
40 % 99 211 234
30 % 99 211 248
Entity #9 | 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 % 95 171 178
95 % 95 171 236 Flexibility: Low
Max RMSD: 1.4, Avg RMSD: 0.6
PDBFlex
90 % 95 171 247
70 % 95 171 278
50 % 96 192 252
40 % 96 192 263
30 % 96 192 281

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