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 % 110 177 238
70 % 110 177 261
50 % 112 196 247
40 % 112 196 256
30 % 112 210 252
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 % 104 132 231
95 % 104 132 314 Flexibility: Low
Max RMSD: 2.9, Avg RMSD: 1.0
PDBFlex
90 % 104 132 323
70 % 106 151 323
50 % 107 153 380
40 % 107 153 395
30 % 107 168 375
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 % 110 176 228 Flexibility: No
Max RMSD: 1.1, Avg RMSD: 0.5
PDBFlex
90 % 110 176 240
70 % 113 210 198
50 % 113 210 219
40 % 113 210 237
30 % 113 210 251
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 % 105 133 310 Flexibility: No
Max RMSD: 1.1, Avg RMSD: 0.5
PDBFlex
90 % 105 133 320
70 % 105 133 364
50 % 107 152 385
40 % 108 154 392
30 % 108 154 404
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 % 108 172 175
95 % 108 172 234 Flexibility: Low
Max RMSD: 2.0, Avg RMSD: 1.0
PDBFlex
90 % 108 172 245
70 % 108 172 274
50 % 110 191 255
40 % 110 191 267
30 % 110 191 283
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 30011
95 % 4 5 16332 Flexibility: Low
Max RMSD: 2.8, Avg RMSD: 1.9
PDBFlex
90 % 4 5 15867
70 % 4 5 14868
50 % 4 6 11425
40 % 4 6 10710
30 % 4 6 9846
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 % 105 131 232
95 % 105 131 316 Flexibility: Low
Max RMSD: 6.8, Avg RMSD: 1.6
PDBFlex
90 % 105 131 325
70 % 107 150 325
50 % 108 152 383
40 % 108 152 396
30 % 108 152 409
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 % 104 132 229
95 % 105 133 309 Flexibility: Low
Max RMSD: 3.3, Avg RMSD: 1.2
PDBFlex
90 % 105 133 319
70 % 108 154 316
50 % 108 167 347
40 % 113 129 315
30 % 113 190 286
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 % 103 128 238
95 % 103 128 329 Flexibility: Low
Max RMSD: 1.0, Avg RMSD: 0.5
PDBFlex
90 % 103 128 336
70 % 103 128 385
50 % 103 128 453
40 % 104 130 463
30 % 104 130 496
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 70 741 Flexibility: Low
Max RMSD: 3.5, Avg RMSD: 0.8
PDBFlex
90 % 51 70 777
70 % 51 71 806
50 % 51 71 861
40 % 51 71 902
30 % 51 71 946
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 % 111 177 226 Flexibility: Low
Max RMSD: 2.1, Avg RMSD: 0.7
PDBFlex
90 % 111 177 239
70 % 113 196 236
50 % 114 198 241
40 % 114 211 234
30 % 114 211 248
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 % 108 171 178
95 % 108 171 236 Flexibility: Low
Max RMSD: 1.4, Avg RMSD: 0.6
PDBFlex
90 % 108 171 247
70 % 108 171 278
50 % 111 192 252
40 % 111 192 263
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 73 516
95 % 53 73 706 Flexibility: Low
Max RMSD: 4.4, Avg RMSD: 0.7
PDBFlex
90 % 53 73 735
70 % 53 73 774
50 % 57 108 489
40 % 57 108 522
30 % 57 108 547

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