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 % 90 116 230
95 % 90 116 324 Flexibility: Low
Max RMSD: 5.3, Avg RMSD: 1.6
PDBFlex
90 % 90 116 342
70 % 92 121 360
50 % 92 133 368
40 % 92 133 394
30 % 92 133 395
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 % 94 143 176
95 % 94 143 238 Flexibility: No
Max RMSD: 1.1, Avg RMSD: 0.5
PDBFlex
90 % 94 143 253
70 % 96 160 256
50 % 101 168 247
40 % 101 168 268
30 % 101 168 274
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 % 90 118 225
95 % 90 118 320 Flexibility: No
Max RMSD: 1.0, Avg RMSD: 0.5
PDBFlex
90 % 90 118 337
70 % 90 118 374
50 % 92 123 415
40 % 92 125 433
30 % 92 125 439
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 % 92 139 184
95 % 92 139 244 Flexibility: Low
Max RMSD: 2.0, Avg RMSD: 1.0
PDBFlex
90 % 92 139 260
70 % 92 139 294
50 % 94 144 315
40 % 94 144 334
30 % 94 144 343
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 % 89 117 226
95 % 90 118 314 Flexibility: Low
Max RMSD: 3.3, Avg RMSD: 1.3
PDBFlex
90 % 90 118 331
70 % 92 125 343
50 % 92 135 360
40 % 97 143 326
30 % 97 146 333
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 % 88 113 233
95 % 88 113 330 Flexibility: Low
Max RMSD: 1.0, Avg RMSD: 0.5
PDBFlex
90 % 88 113 350
70 % 88 113 382
50 % 88 115 444
40 % 88 115 476
30 % 88 115 473
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 62 560
95 % 47 62 766 Flexibility: Low
Max RMSD: 3.5, Avg RMSD: 0.7
PDBFlex
90 % 47 62 797
70 % 47 63 826
50 % 50 70 750
40 % 50 70 788
30 % 50 70 780
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 % 95 144 173
95 % 95 144 235 Flexibility: Low
Max RMSD: 2.1, Avg RMSD: 0.7
PDBFlex
90 % 95 144 250
70 % 97 149 275
50 % 97 151 295
40 % 97 161 290
30 % 97 161 296
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 % 92 138 187
95 % 92 138 250 Flexibility: Low
Max RMSD: 1.4, Avg RMSD: 0.6
PDBFlex
90 % 92 138 264
70 % 92 138 297
50 % 94 156 282
40 % 94 156 301
30 % 94 156 309
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 65 514
95 % 49 65 701 Flexibility: Low
Max RMSD: 4.2, Avg RMSD: 0.7
PDBFlex
90 % 49 65 730
70 % 49 65 786
50 % 52 83 569
40 % 52 83 609
30 % 52 83 597
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 % 93 143 175
95 % 94 144 236
90 % 94 144 251
70 % 94 144 284
50 % 96 149 304
40 % 96 149 317
30 % 96 162 293
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 % 89 117 228
95 % 89 117 322
90 % 89 117 340
70 % 91 122 359
50 % 91 124 410
40 % 91 124 440
30 % 91 127 429

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.