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 % 100 115 226
95 % 100 115 318 Flexibility: Low
Max RMSD: 6.8, Avg RMSD: 1.6
PDBFlex
90 % 100 115 335
70 % 102 120 352
50 % 103 131 363
40 % 103 131 387
30 % 103 131 395
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 % 105 142 173
95 % 105 142 233 Flexibility: No
Max RMSD: 1.1, Avg RMSD: 0.5
PDBFlex
90 % 105 142 248
70 % 108 158 251
50 % 114 166 247
40 % 114 166 264
30 % 114 166 271
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 Structural variation in cluster
100 % 100 117 221
95 % 100 117 311 Flexibility: No
Max RMSD: 1.1, Avg RMSD: 0.5
PDBFlex
90 % 100 117 328
70 % 100 117 365
50 % 102 122 410
40 % 103 124 426
30 % 103 124 427
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 % 103 138 180
95 % 103 138 242 Flexibility: Low
Max RMSD: 2.0, Avg RMSD: 1.0
PDBFlex
90 % 103 138 256
70 % 103 138 286
50 % 105 143 309
40 % 105 143 321
30 % 105 143 334
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 % 99 116 223
95 % 100 117 308 Flexibility: Low
Max RMSD: 3.3, Avg RMSD: 1.3
PDBFlex
90 % 100 117 324
70 % 103 124 332
50 % 103 133 349
40 % 109 141 322
30 % 109 144 328
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 % 98 112 230
95 % 98 112 322 Flexibility: Low
Max RMSD: 1.0, Avg RMSD: 0.5
PDBFlex
90 % 98 112 341
70 % 98 112 376
50 % 99 114 437
40 % 99 114 465
30 % 99 114 467
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 Structural variation in cluster
100 % 51 61 562
95 % 51 61 780 Flexibility: Low
Max RMSD: 3.5, Avg RMSD: 0.7
PDBFlex
90 % 51 61 808
70 % 51 62 832
50 % 54 69 749
40 % 54 69 778
30 % 54 69 773
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 % 106 143 170
95 % 106 143 231 Flexibility: Low
Max RMSD: 2.1, Avg RMSD: 0.7
PDBFlex
90 % 106 143 246
70 % 108 148 268
50 % 109 150 289
40 % 109 159 285
30 % 109 159 293
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 % 103 137 183
95 % 103 137 245 Flexibility: Low
Max RMSD: 1.4, Avg RMSD: 0.6
PDBFlex
90 % 103 137 259
70 % 103 137 290
50 % 106 154 281
40 % 106 154 297
30 % 106 154 308
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 64 514
95 % 53 64 706 Flexibility: Low
Max RMSD: 4.4, Avg RMSD: 0.6
PDBFlex
90 % 53 64 735
70 % 53 64 788
50 % 57 81 569
40 % 57 81 609
30 % 57 81 604
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 % 104 142 172
95 % 105 143 232 Flexibility: Low
Max RMSD: 1.9, Avg RMSD: 0.9
PDBFlex
90 % 105 143 247
70 % 105 143 277
50 % 107 148 293
40 % 107 148 307
30 % 108 160 292
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 % 99 116 225
95 % 99 116 317 Flexibility: Low
Max RMSD: 2.9, Avg RMSD: 1.0
PDBFlex
90 % 99 116 334
70 % 101 121 351
50 % 102 123 402
40 % 102 123 431
30 % 102 126 420

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.