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 % 95 124 228
95 % 95 124 317 Flexibility: Low
Max RMSD: 5.3, Avg RMSD: 1.6
PDBFlex
90 % 95 124 330
70 % 97 129 355
50 % 97 142 377
40 % 97 142 395
30 % 97 142 399
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 % 99 159 174
95 % 99 159 235 Flexibility: No
Max RMSD: 1.1, Avg RMSD: 0.5
PDBFlex
90 % 99 159 247
70 % 101 177 236
50 % 106 185 230
40 % 106 185 249
30 % 106 185 259
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 % 95 126 220
95 % 95 126 313 Flexibility: No
Max RMSD: 1.0, Avg RMSD: 0.5
PDBFlex
90 % 95 126 325
70 % 95 126 373
50 % 97 131 416
40 % 97 133 426
30 % 97 133 426
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 % 97 155 176
95 % 97 155 240 Flexibility: Low
Max RMSD: 2.0, Avg RMSD: 1.0
PDBFlex
90 % 97 155 252
70 % 97 155 284
50 % 99 160 291
40 % 99 160 313
30 % 99 160 319
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 % 94 125 223
95 % 95 126 309 Flexibility: Low
Max RMSD: 3.3, Avg RMSD: 1.3
PDBFlex
90 % 95 126 321
70 % 97 133 336
50 % 97 144 372
40 % 102 152 338
30 % 102 163 306
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 % 93 121 235
95 % 93 121 324 Flexibility: Low
Max RMSD: 1.0, Avg RMSD: 0.5
PDBFlex
90 % 93 121 340
70 % 93 121 382
50 % 93 123 439
40 % 93 123 464
30 % 93 123 460
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 65 554
95 % 47 65 751 Flexibility: Low
Max RMSD: 3.5, Avg RMSD: 0.7
PDBFlex
90 % 47 65 780
70 % 47 66 806
50 % 50 73 746
40 % 50 73 778
30 % 50 73 776
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 % 100 160 171
95 % 100 160 230 Flexibility: Low
Max RMSD: 2.1, Avg RMSD: 0.7
PDBFlex
90 % 100 160 241
70 % 102 165 257
50 % 102 167 273
40 % 102 178 266
30 % 102 178 280
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 % 97 154 177
95 % 97 154 241 Flexibility: Low
Max RMSD: 1.4, Avg RMSD: 0.6
PDBFlex
90 % 97 154 253
70 % 97 154 285
50 % 99 173 262
40 % 99 173 273
30 % 99 173 286
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 68 500
95 % 49 68 686 Flexibility: Low
Max RMSD: 4.2, Avg RMSD: 0.7
PDBFlex
90 % 49 68 715
70 % 49 68 760
50 % 52 87 562
40 % 52 87 599
30 % 52 87 591
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 % 98 159 173
95 % 99 160 232
90 % 99 160 243
70 % 99 160 272
50 % 101 165 283
40 % 101 165 299
30 % 101 179 278
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 % 94 125 227
95 % 94 125 316
90 % 94 125 329
70 % 96 130 354
50 % 96 132 410
40 % 96 132 430
30 % 96 143 397

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