Sequence Similarity Clusters for the Entities in PDB 2JA6

Entity #1 | 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 % 101 118 230
95 % 101 118 320 Flexibility: Low
Max RMSD: 5.3, Avg RMSD: 1.6
PDBFlex
90 % 101 118 336
70 % 103 123 357
50 % 104 135 365
40 % 104 135 389
30 % 104 135 387
Entity #10 | 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 % 106 145 177
95 % 106 145 239 Flexibility: No
Max RMSD: 1.1, Avg RMSD: 0.5
PDBFlex
90 % 106 145 254
70 % 109 162 251
50 % 115 170 245
40 % 115 170 266
30 % 115 170 271
Entity #11 | 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 % 101 120 224
95 % 101 120 315
90 % 101 120 330
70 % 101 120 371
50 % 103 125 412
40 % 104 127 425
30 % 104 127 431
Entity #12 | 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 % 104 141 182
95 % 104 141 245 Flexibility: Low
Max RMSD: 2.0, Avg RMSD: 1.0
PDBFlex
90 % 104 141 261
70 % 104 141 293
50 % 106 146 311
40 % 106 146 329
30 % 106 146 338
Entity #13 | Chains: N
5'-D(*TP*AP*AP*GP*TP*AP*CP*TP*TP*GP *AP*GP*CP*T)-3' dna, length: 14 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
Entity #14 | Chains: P
5'-R(*UP*UP*CP*GP*AP*CP*CP*AP*GP*GP*AP)-3' rna, length: 11 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
Entity #15 | Chains: T
5'-D(*AP*GP*CP*TP*CP*AP*AP*GP*TP*AP *CP*TP*TP*TTP*TP*CP*CP*BRUP*GP*GP*TP*CP*AP*TP*T)-3' dna, length: 25 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
Entity #2 | 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 % 100 119 225
95 % 101 120 313 Flexibility: Low
Max RMSD: 3.3, Avg RMSD: 1.3
PDBFlex
90 % 101 120 327
70 % 104 127 333
50 % 104 137 353
40 % 110 145 328
30 % 110 148 328
Entity #3 | Chains: C
DNA-DIRECTED RNA POLYMERASE II 45KDA POLYPEPTIDE protein, length: 318 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name Structural variation in cluster
100 % 99 115 233
95 % 99 115 330 Flexibility: Low
Max RMSD: 1.0, Avg RMSD: 0.5
PDBFlex
90 % 99 115 348
70 % 99 115 381
50 % 100 117 442
40 % 100 117 471
30 % 100 117 467
Entity #4 | Chains: D
DNA-DIRECTED RNA POLYMERASE II 32KDA POLYPEPTIDE protein, length: 221 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 52 64 544
95 % 52 64 736
90 % 52 64 766
70 % 52 65 806
50 % 55 72 727
40 % 55 72 762
30 % 55 72 754
Entity #5 | 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 % 107 146 175
95 % 107 146 236 Flexibility: Low
Max RMSD: 2.1, Avg RMSD: 0.7
PDBFlex
90 % 107 146 250
70 % 109 151 276
50 % 110 153 290
40 % 110 163 288
30 % 110 163 294
Entity #6 | 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 % 104 140 183
95 % 104 140 247 Flexibility: Low
Max RMSD: 1.4, Avg RMSD: 0.6
PDBFlex
90 % 104 140 262
70 % 104 140 295
50 % 107 158 276
40 % 107 158 294
30 % 107 158 301
Entity #7 | Chains: G
DNA-DIRECTED RNA POLYMERASE II 19KDA POLYPEPTIDE protein, length: 171 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name Structural variation in cluster
100 % 54 67 489
95 % 54 67 678 Flexibility: Low
Max RMSD: 4.2, Avg RMSD: 0.7
PDBFlex
90 % 54 67 706
70 % 54 67 758
50 % 58 85 560
40 % 58 85 599
30 % 58 85 590
Entity #8 | 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 % 105 145 176
95 % 106 146 237 Flexibility: Low
Max RMSD: 1.9, Avg RMSD: 1.0
PDBFlex
90 % 106 146 251
70 % 106 146 284
50 % 108 151 302
40 % 108 151 314
30 % 109 164 291
Entity #9 | 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 % 100 119 229
95 % 100 119 318 Flexibility: Low
Max RMSD: 2.9, Avg RMSD: 1.0
PDBFlex
90 % 100 119 334
70 % 102 124 355
50 % 103 126 401
40 % 103 126 431
30 % 103 129 422

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.