Sequence Similarity Clusters for the Entities in PDB 2JA7

Entity #1 | Chains: 1,4
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 #10 | Chains: G,S
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 % 44 64 514
95 % 44 64 706 Flexibility: Low
Max RMSD: 4.4, Avg RMSD: 0.6
PDBFlex
90 % 44 64 735
70 % 44 64 788
50 % 46 81 569
40 % 46 81 609
30 % 46 81 604
Entity #11 | Chains: H,T
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 % 85 142 172
95 % 86 143 232 Flexibility: Low
Max RMSD: 1.9, Avg RMSD: 0.9
PDBFlex
90 % 86 143 247
70 % 86 143 277
50 % 87 148 293
40 % 87 148 307
30 % 87 160 292
Entity #12 | Chains: I,U
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 % 82 116 225
95 % 82 116 317 Flexibility: Low
Max RMSD: 2.9, Avg RMSD: 1.0
PDBFlex
90 % 82 116 334
70 % 83 121 351
50 % 83 123 402
40 % 83 123 431
30 % 83 126 420
Entity #13 | Chains: J,V
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 % 86 142 173
95 % 86 142 233 Flexibility: No
Max RMSD: 1.1, Avg RMSD: 0.5
PDBFlex
90 % 86 142 248
70 % 87 158 251
50 % 92 166 247
40 % 92 166 264
30 % 92 166 271
Entity #14 | Chains: K,W
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 % 82 117 221
95 % 82 117 311 Flexibility: No
Max RMSD: 1.1, Avg RMSD: 0.5
PDBFlex
90 % 82 117 328
70 % 82 117 365
50 % 83 122 410
40 % 83 124 426
30 % 83 124 427
Entity #15 | Chains: L,X
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 % 84 138 180
95 % 84 138 242 Flexibility: Low
Max RMSD: 2.0, Avg RMSD: 1.0
PDBFlex
90 % 84 138 256
70 % 84 138 286
50 % 85 143 309
40 % 85 143 321
30 % 85 143 334
Entity #2 | Chains: 2,5
5'-D(*AP*GP*CP*TP*CP*AP*AP*GP*TP*AP *CP*TP*TP*TP*TTP*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 #3 | Chains: 3,6
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 #4 | Chains: A,M
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 % 82 115 226
95 % 82 115 318 Flexibility: Low
Max RMSD: 6.8, Avg RMSD: 1.6
PDBFlex
90 % 82 115 335
70 % 83 120 352
50 % 83 131 363
40 % 83 131 387
30 % 83 131 395
Entity #5 | Chains: B,N
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 % 81 116 223
95 % 82 117 308 Flexibility: Low
Max RMSD: 3.3, Avg RMSD: 1.3
PDBFlex
90 % 82 117 324
70 % 83 124 332
50 % 83 133 349
40 % 88 141 322
30 % 88 144 328
Entity #6 | Chains: C,O
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 % 80 112 230
95 % 80 112 322 Flexibility: Low
Max RMSD: 1.0, Avg RMSD: 0.5
PDBFlex
90 % 80 112 341
70 % 80 112 376
50 % 80 114 437
40 % 80 114 465
30 % 80 114 467
Entity #7 | Chains: D,P
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 % 42 61 562
95 % 42 61 780 Flexibility: Low
Max RMSD: 3.5, Avg RMSD: 0.7
PDBFlex
90 % 42 61 808
70 % 42 62 832
50 % 44 69 749
40 % 44 69 778
30 % 44 69 773
Entity #8 | Chains: E,Q
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 % 87 143 170
95 % 87 143 231 Flexibility: Low
Max RMSD: 2.1, Avg RMSD: 0.7
PDBFlex
90 % 87 143 246
70 % 88 148 268
50 % 88 150 289
40 % 88 159 285
30 % 88 159 293
Entity #9 | Chains: F,R
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 % 84 137 183
95 % 84 137 245 Flexibility: Low
Max RMSD: 1.4, Avg RMSD: 0.6
PDBFlex
90 % 84 137 259
70 % 84 137 290
50 % 85 154 281
40 % 85 154 297
30 % 85 154 308

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.