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
100 % 100 115 230
95 % 100 115 322
90 % 100 115 341
70 % 102 120 357
50 % 103 132 369
40 % 103 132 394
30 % 103 132 399
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 % 105 142 176
95 % 105 142 236 Flexibility: No
Max RMSD: 1.1, Avg RMSD: 0.5
PDBFlex
90 % 105 142 250
70 % 108 159 251
50 % 114 167 247
40 % 114 167 266
30 % 114 167 272
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 Structural variation in cluster
100 % 100 117 224
95 % 100 117 316 Flexibility: No
Max RMSD: 1.1, Avg RMSD: 0.5
PDBFlex
90 % 100 117 334
70 % 100 117 370
50 % 102 122 416
40 % 103 124 435
30 % 103 124 436
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
100 % 103 138 185
95 % 103 138 245
90 % 103 138 260
70 % 103 138 290
50 % 105 143 313
40 % 105 143 331
30 % 105 143 338
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 % 99 116 226
95 % 100 117 314 Flexibility: Low
Max RMSD: 3.3, Avg RMSD: 1.3
PDBFlex
90 % 100 117 331
70 % 103 124 342
50 % 103 134 357
40 % 109 142 327
30 % 109 145 331
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 % 98 112 233
95 % 98 112 328 Flexibility: Low
Max RMSD: 1.0, Avg RMSD: 0.5
PDBFlex
90 % 98 112 347
70 % 98 112 380
50 % 99 114 441
40 % 99 114 473
30 % 99 114 472
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 Structural variation in cluster
100 % 51 61 566
95 % 51 61 782 Flexibility: Low
Max RMSD: 3.5, Avg RMSD: 0.8
PDBFlex
90 % 51 61 810
70 % 51 62 835
50 % 54 69 754
40 % 54 69 787
30 % 54 69 780
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
100 % 106 143 173
95 % 106 143 233
90 % 106 143 248
70 % 108 148 272
50 % 109 150 291
40 % 109 160 286
30 % 109 160 293
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 % 103 137 188
95 % 103 137 248 Flexibility: Low
Max RMSD: 1.4, Avg RMSD: 0.6
PDBFlex
90 % 103 137 263
70 % 103 137 294
50 % 106 155 279
40 % 106 155 298
30 % 106 155 309
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 % 53 64 525
95 % 53 64 717 Flexibility: Low
Max RMSD: 4.4, Avg RMSD: 0.8
PDBFlex
90 % 53 64 747
70 % 53 64 798
50 % 57 82 570
40 % 57 82 607
30 % 57 82 597
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 % 104 142 175
95 % 105 143 234 Flexibility: Low
Max RMSD: 1.9, Avg RMSD: 0.9
PDBFlex
90 % 105 143 249
70 % 105 143 281
50 % 107 148 299
40 % 107 148 314
30 % 108 161 292
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 % 99 116 228
95 % 99 116 321 Flexibility: Low
Max RMSD: 2.7, Avg RMSD: 0.9
PDBFlex
90 % 99 116 340
70 % 101 121 356
50 % 102 123 407
40 % 102 123 437
30 % 102 126 427

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.