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 % 89 115 226
95 % 89 115 317 Flexibility: Low
Max RMSD: 6.8, Avg RMSD: 1.7
PDBFlex
90 % 89 115 334
70 % 90 118 356
50 % 90 129 371
40 % 90 129 398
30 % 90 129 405
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 % 93 141 175
95 % 93 141 234 Flexibility: No
Max RMSD: 1.1, Avg RMSD: 0.5
PDBFlex
90 % 93 141 250
70 % 94 155 255
50 % 99 163 251
40 % 99 163 268
30 % 99 163 278
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 % 89 117 221
95 % 89 117 310 Flexibility: No
Max RMSD: 1.1, Avg RMSD: 0.5
PDBFlex
90 % 89 117 327
70 % 89 117 365
50 % 90 120 412
40 % 90 122 429
30 % 90 122 433
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 % 91 137 183
95 % 91 137 245 Flexibility: Low
Max RMSD: 2.0, Avg RMSD: 1.0
PDBFlex
90 % 91 137 258
70 % 91 137 289
50 % 92 140 313
40 % 92 140 329
30 % 92 140 338
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 % 88 116 223
95 % 89 117 308 Flexibility: Low
Max RMSD: 3.3, Avg RMSD: 1.2
PDBFlex
90 % 89 117 324
70 % 90 122 341
50 % 90 131 360
40 % 95 139 325
30 % 95 142 331
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 % 87 112 230
95 % 87 112 322 Flexibility: Low
Max RMSD: 1.0, Avg RMSD: 0.5
PDBFlex
90 % 87 112 341
70 % 87 112 377
50 % 87 114 437
40 % 87 114 464
30 % 87 114 465
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 % 46 61 559
95 % 46 61 775 Flexibility: Low
Max RMSD: 3.5, Avg RMSD: 0.7
PDBFlex
90 % 46 61 803
70 % 46 62 828
50 % 48 67 755
40 % 48 67 786
30 % 48 67 780
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
100 % 94 142 171
95 % 94 142 231
90 % 94 142 246
70 % 95 145 272
50 % 95 147 292
40 % 95 156 292
30 % 95 156 298
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 % 91 136 185
95 % 91 136 247 Flexibility: Low
Max RMSD: 1.4, Avg RMSD: 0.6
PDBFlex
90 % 91 136 261
70 % 91 136 291
50 % 92 151 284
40 % 92 151 300
30 % 92 151 315
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 % 48 64 506
95 % 48 64 701 Flexibility: Low
Max RMSD: 4.4, Avg RMSD: 0.8
PDBFlex
90 % 48 64 731
70 % 48 64 784
50 % 50 79 582
40 % 50 79 619
30 % 50 79 614
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 Structural variation in cluster
100 % 92 141 174
95 % 93 142 232 Flexibility: Low
Max RMSD: 1.9, Avg RMSD: 1.0
PDBFlex
90 % 93 142 247
70 % 93 142 279
50 % 94 145 301
40 % 94 145 310
30 % 94 157 293
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 Structural variation in cluster
100 % 88 116 225
95 % 88 116 316 Flexibility: Low
Max RMSD: 2.9, Avg RMSD: 1.0
PDBFlex
90 % 88 116 333
70 % 89 119 354
50 % 89 121 407
40 % 89 121 433
30 % 89 124 426

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.