Sequence Similarity Clusters for the Entities in PDB 2JA5

Entity #1 | Chains: A
DNA-directed RNA polymerase II subunit RPB1 protein, length: 1733 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name Structural variation in cluster
100 % 90 118 251
95 % 90 118 326 Flexibility: Low
Max RMSD: 5.3, Avg RMSD: 1.6
PDBFlex
90 % 90 118 342
70 % 92 123 364
50 % 92 135 384
40 % 92 135 417
30 % 92 135 425
Entity #10 | Chains: J
DNA-directed RNA polymerases I, II, and III subunit RPABC5 protein, length: 70 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name Structural variation in cluster
100 % 94 153 185
95 % 94 153 238 Flexibility: No
Max RMSD: 1.1, Avg RMSD: 0.5
PDBFlex
90 % 94 153 245
70 % 96 170 242
50 % 101 178 234
40 % 101 178 262
30 % 101 178 275
Entity #11 | Chains: K
DNA-directed RNA polymerase II subunit RPB11 protein, length: 120 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name Structural variation in cluster
100 % 90 120 240
95 % 90 120 319 Flexibility: No
Max RMSD: 1.0, Avg RMSD: 0.5
PDBFlex
90 % 90 120 333
70 % 90 120 377
50 % 92 125 419
40 % 92 127 438
30 % 92 127 450
Entity #12 | Chains: L
DNA-directed RNA polymerases I, II, and III subunit RPABC4 protein, length: 70 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name Structural variation in cluster
100 % 92 149 192
95 % 92 149 243 Flexibility: Low
Max RMSD: 2.0, Avg RMSD: 1.0
PDBFlex
90 % 92 149 250
70 % 92 149 286
50 % 94 154 298
40 % 94 154 328
30 % 94 154 334
Entity #13 | 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 #14 | Chains: T
5'-D(*AP*GP*CP*TP*CP*AP*AP*GP*TP*AP *CP*TP*TTP*TP*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 subunit RPB2 protein, length: 1224 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name Structural variation in cluster
100 % 90 120 243
95 % 90 120 320 Flexibility: Low
Max RMSD: 3.3, Avg RMSD: 1.3
PDBFlex
90 % 90 120 335
70 % 92 127 347
50 % 92 137 373
40 % 97 145 359
30 % 184 286 148
Entity #3 | Chains: C
DNA-directed RNA polymerase II subunit RPB3 protein, length: 318 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name Structural variation in cluster
100 % 88 115 256
95 % 88 115 332 Flexibility: Low
Max RMSD: 1.0, Avg RMSD: 0.5
PDBFlex
90 % 88 115 349
70 % 88 115 388
50 % 88 115 452
40 % 88 115 499
30 % 88 115 499
Entity #4 | Chains: D
DNA-directed RNA polymerase II subunit RPB4 protein, length: 221 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name Structural variation in cluster
100 % 47 64 611
95 % 47 64 750 Flexibility: Low
Max RMSD: 3.5, Avg RMSD: 0.7
PDBFlex
90 % 47 64 777
70 % 48 67 777
50 % 50 72 745
40 % 50 72 780
30 % 50 72 780
Entity #5 | Chains: E
DNA-directed RNA polymerases I, II, and III subunit RPABC1 protein, length: 215 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name Structural variation in cluster
100 % 95 154 184
95 % 95 154 237 Flexibility: Low
Max RMSD: 2.1, Avg RMSD: 0.7
PDBFlex
90 % 95 154 243
70 % 97 159 265
50 % 97 161 278
40 % 97 171 286
30 % 97 171 301
Entity #6 | Chains: F
DNA-directed RNA polymerases I, II, and III subunit RPABC2 protein, length: 155 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name Structural variation in cluster
100 % 92 148 194
95 % 92 148 244 Flexibility: Low
Max RMSD: 1.4, Avg RMSD: 0.6
PDBFlex
90 % 92 148 251
70 % 92 148 288
50 % 94 166 268
40 % 94 166 297
30 % 94 166 312
Entity #7 | Chains: G
DNA-directed RNA polymerase II subunit RPB7 protein, length: 171 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name Structural variation in cluster
100 % 49 67 547
95 % 49 67 685 Flexibility: Low
Max RMSD: 4.2, Avg RMSD: 0.7
PDBFlex
90 % 49 67 713
70 % 49 67 753
50 % 52 85 569
40 % 52 85 610
30 % 52 85 604
Entity #8 | Chains: H
DNA-directed RNA polymerases I, II, and III subunit RPABC3 protein, length: 146 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 93 153 188
95 % 94 154 236
90 % 94 154 244
70 % 94 154 278
50 % 96 159 286
40 % 96 159 318
30 % 96 172 298
Entity #9 | Chains: I
DNA-directed RNA polymerase II subunit RPB9 protein, length: 122 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 89 119 245
95 % 89 119 322
90 % 89 119 337
70 % 91 124 363
50 % 91 126 413
40 % 91 126 447
30 % 91 137 410

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