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 64 524
95 % 44 64 715 Flexibility: Low
Max RMSD: 4.4, Avg RMSD: 0.8
PDBFlex
90 % 44 64 745
70 % 44 64 797
50 % 46 82 567
40 % 46 82 605
30 % 46 82 595
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 % 85 142 174
95 % 86 143 234 Flexibility: Low
Max RMSD: 1.9, Avg RMSD: 0.9
PDBFlex
90 % 86 143 249
70 % 86 143 281
50 % 87 148 298
40 % 87 148 314
30 % 87 161 292
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 % 82 116 228
95 % 82 116 321 Flexibility: Low
Max RMSD: 2.9, Avg RMSD: 1.0
PDBFlex
90 % 82 116 339
70 % 83 121 356
50 % 83 123 406
40 % 83 123 437
30 % 83 126 427
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 % 86 142 175
95 % 86 142 236 Flexibility: No
Max RMSD: 1.1, Avg RMSD: 0.5
PDBFlex
90 % 86 142 250
70 % 87 159 251
50 % 92 167 247
40 % 92 167 265
30 % 92 167 271
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 % 82 117 224
95 % 82 117 316 Flexibility: No
Max RMSD: 1.1, Avg RMSD: 0.5
PDBFlex
90 % 82 117 334
70 % 82 117 370
50 % 83 122 416
40 % 83 124 434
30 % 83 124 436
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 % 84 138 184
95 % 84 138 245 Flexibility: Low
Max RMSD: 2.0, Avg RMSD: 1.0
PDBFlex
90 % 84 138 260
70 % 84 138 290
50 % 85 143 313
40 % 85 143 330
30 % 85 143 337
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 % 82 115 229
95 % 82 115 322 Flexibility: Low
Max RMSD: 6.8, Avg RMSD: 1.5
PDBFlex
90 % 82 115 340
70 % 83 120 357
50 % 83 132 369
40 % 83 132 394
30 % 83 132 399
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 % 81 116 226
95 % 82 117 314 Flexibility: Low
Max RMSD: 3.3, Avg RMSD: 1.3
PDBFlex
90 % 82 117 331
70 % 83 124 341
50 % 83 134 357
40 % 88 142 326
30 % 88 145 331
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 % 80 112 233
95 % 80 112 327 Flexibility: Low
Max RMSD: 1.0, Avg RMSD: 0.5
PDBFlex
90 % 80 112 346
70 % 80 112 379
50 % 80 114 440
40 % 80 114 472
30 % 80 114 472
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 61 565
95 % 42 61 781 Flexibility: Low
Max RMSD: 3.5, Avg RMSD: 0.8
PDBFlex
90 % 42 61 809
70 % 42 62 835
50 % 44 69 753
40 % 44 69 786
30 % 44 69 779
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 % 87 143 172
95 % 87 143 233 Flexibility: Low
Max RMSD: 2.1, Avg RMSD: 0.7
PDBFlex
90 % 87 143 248
70 % 88 148 271
50 % 88 150 290
40 % 88 160 286
30 % 88 160 293
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 % 84 137 187
95 % 84 137 248 Flexibility: Low
Max RMSD: 1.4, Avg RMSD: 0.6
PDBFlex
90 % 84 137 263
70 % 84 137 294
50 % 85 155 279
40 % 85 155 298
30 % 85 155 309

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.