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 % 108 132 262
95 % 108 132 352 Flexibility: Low
Max RMSD: 6.8, Avg RMSD: 1.6
PDBFlex
90 % 108 132 369
70 % 110 151 350
50 % 111 153 401
40 % 111 153 426
30 % 111 153 438
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 % 113 177 187
95 % 113 177 246 Flexibility: No
Max RMSD: 1.1, Avg RMSD: 0.5
PDBFlex
90 % 113 177 257
70 % 116 213 240
50 % 116 213 248
40 % 116 213 262
30 % 116 213 281
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 % 108 134 252
95 % 108 134 339 Flexibility: No
Max RMSD: 1.1, Avg RMSD: 0.5
PDBFlex
90 % 108 134 355
70 % 108 134 391
50 % 110 153 406
40 % 111 155 420
30 % 111 155 430
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 % 111 173 191
95 % 111 173 250 Flexibility: Low
Max RMSD: 2.0, Avg RMSD: 1.0
PDBFlex
90 % 111 173 262
70 % 111 173 302
50 % 113 192 314
40 % 113 192 328
30 % 113 192 346
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 % 107 133 254
95 % 108 134 338 Flexibility: Low
Max RMSD: 3.3, Avg RMSD: 1.2
PDBFlex
90 % 108 134 354
70 % 111 155 339
50 % 111 170 361
40 % 117 178 353
30 % 117 193 339
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 % 106 129 279
95 % 106 129 373 Flexibility: Low
Max RMSD: 1.0, Avg RMSD: 0.5
PDBFlex
90 % 106 129 388
70 % 106 129 420
50 % 106 129 468
40 % 107 131 491
30 % 107 131 519
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 % 52 70 614
95 % 52 70 837 Flexibility: Low
Max RMSD: 3.5, Avg RMSD: 0.8
PDBFlex
90 % 52 70 872
70 % 52 71 895
50 % 52 71 919
40 % 52 71 960
30 % 52 71 999
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 % 114 178 185
95 % 114 178 244 Flexibility: Low
Max RMSD: 2.1, Avg RMSD: 0.7
PDBFlex
90 % 114 178 254
70 % 116 197 263
50 % 117 199 290
40 % 117 214 259
30 % 117 214 278
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 % 111 172 192
95 % 111 172 251 Flexibility: Low
Max RMSD: 1.4, Avg RMSD: 0.6
PDBFlex
90 % 111 172 263
70 % 111 172 303
50 % 114 193 307
40 % 114 193 321
30 % 114 193 336
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 73 560
95 % 54 73 765 Flexibility: Low
Max RMSD: 4.4, Avg RMSD: 0.7
PDBFlex
90 % 54 73 807
70 % 54 73 844
50 % 58 110 518
40 % 58 110 554
30 % 58 110 575
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 % 112 177 186
95 % 113 178 243 Flexibility: Low
Max RMSD: 1.9, Avg RMSD: 1.0
PDBFlex
90 % 113 178 253
70 % 113 178 292
50 % 115 197 300
40 % 115 197 311
30 % 115 213 288
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 % 107 133 258
95 % 107 133 347 Flexibility: Low
Max RMSD: 2.9, Avg RMSD: 1.0
PDBFlex
90 % 107 133 367
70 % 109 152 346
50 % 110 154 397
40 % 110 169 389
30 % 110 184 367

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