Sequence Similarity Clusters for the Entities in PDB 1Y77

Entity #1 | Chains: T
5'-D(P*AP*GP*TP*AP*CP*TP*TP*AP*CP*T*CP*GP*CP*CP*TP*GP*GP*TP*CP*TP*G)-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 % 55 67 498
95 % 55 67 690 Flexibility: Low
Max RMSD: 4.2, Avg RMSD: 0.7
PDBFlex
90 % 55 67 720
70 % 55 67 762
50 % 59 85 568
40 % 59 85 605
30 % 59 85 596
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 % 107 153 174
95 % 108 154 233 Flexibility: Low
Max RMSD: 1.9, Avg RMSD: 1.0
PDBFlex
90 % 108 154 245
70 % 108 154 279
50 % 110 159 284
40 % 110 159 300
30 % 111 172 280
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 % 102 119 234
95 % 102 119 321 Flexibility: Low
Max RMSD: 2.9, Avg RMSD: 1.0
PDBFlex
90 % 102 119 339
70 % 104 124 365
50 % 105 126 412
40 % 105 126 442
30 % 105 137 400
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 % 108 153 175
95 % 108 153 238 Flexibility: No
Max RMSD: 1.1, Avg RMSD: 0.5
PDBFlex
90 % 108 153 250
70 % 111 170 246
50 % 119 178 235
40 % 119 178 254
30 % 119 178 260
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
100 % 103 120 229
95 % 103 120 319
90 % 103 120 336
70 % 103 120 378
50 % 105 125 423
40 % 106 127 437
30 % 106 127 441
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
100 % 106 149 181
95 % 106 149 241
90 % 106 149 254
70 % 106 149 288
50 % 108 154 300
40 % 108 154 318
30 % 108 154 323
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 % 103 118 235
95 % 103 118 323 Flexibility: Low
Max RMSD: 5.3, Avg RMSD: 1.6
PDBFlex
90 % 103 118 341
70 % 105 123 366
50 % 106 135 382
40 % 106 135 408
30 % 106 135 409
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 % 102 119 230
95 % 103 120 317 Flexibility: Low
Max RMSD: 3.3, Avg RMSD: 1.3
PDBFlex
90 % 103 120 333
70 % 106 127 346
50 % 106 137 374
40 % 114 145 343
30 % 114 156 312
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 % 101 115 237
95 % 101 115 332 Flexibility: Low
Max RMSD: 1.0, Avg RMSD: 0.5
PDBFlex
90 % 101 115 352
70 % 101 115 386
50 % 102 117 447
40 % 102 117 476
30 % 102 117 469
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 % 53 64 555
95 % 53 64 748 Flexibility: Low
Max RMSD: 3.5, Avg RMSD: 0.7
PDBFlex
90 % 53 64 778
70 % 53 65 812
50 % 56 72 738
40 % 56 72 774
30 % 56 72 766
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 % 109 154 171
95 % 109 154 232 Flexibility: Low
Max RMSD: 2.1, Avg RMSD: 0.7
PDBFlex
90 % 109 154 244
70 % 111 159 266
50 % 112 161 279
40 % 112 171 274
30 % 112 171 282
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 % 106 148 182
95 % 106 148 243 Flexibility: Low
Max RMSD: 1.4, Avg RMSD: 0.6
PDBFlex
90 % 106 148 256
70 % 106 148 290
50 % 109 166 270
40 % 109 166 285
30 % 109 166 295

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