Sequence Similarity Clusters for the Entities in PDB 4A3J

Entity #1 | Chains: A
DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB1 protein, length: 1732 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name Structural variation in cluster
100 % 32 115 229
95 % 32 115 322 Flexibility: Low
Max RMSD: 6.8, Avg RMSD: 1.5
PDBFlex
90 % 32 115 340
70 % 33 120 357
50 % 33 132 369
40 % 33 132 394
30 % 33 132 399
Entity #10 | Chains: J
DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 5 protein, length: 70 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name Structural variation in cluster
100 % 34 142 175
95 % 34 142 236 Flexibility: No
Max RMSD: 1.1, Avg RMSD: 0.5
PDBFlex
90 % 34 142 250
70 % 35 159 251
50 % 35 167 247
40 % 35 167 265
30 % 35 167 271
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 % 32 117 224
95 % 32 117 316 Flexibility: No
Max RMSD: 1.1, Avg RMSD: 0.5
PDBFlex
90 % 32 117 334
70 % 32 117 370
50 % 33 122 416
40 % 33 124 434
30 % 33 124 436
Entity #12 | Chains: L
DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 4 protein, length: 70 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name Structural variation in cluster
100 % 33 138 184
95 % 33 138 245 Flexibility: Low
Max RMSD: 2.0, Avg RMSD: 1.0
PDBFlex
90 % 33 138 260
70 % 33 138 290
50 % 34 143 313
40 % 34 143 330
30 % 34 143 337
Entity #13 | Chains: N
5'-D(*GP*TP*AP*GP*AP*AP*AP*GP*CP*TP*AP*GP*CP*TP)-3' dna, length: 14 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
Entity #14 | Chains: P
5'-R(*CP*AP)-3' rna, length: 2 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
Entity #15 | Chains: T
5'-D(*AP*GP*CP*TP*AP*GP*CP*TP*TP*TP*CP*BRUP*AP*CP*CP *TP*GP*AP*AP*CP*AP*AP*CP*TP*AP*AP*CP)-3' dna, length: 27 (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
100 % 32 116 226
95 % 32 117 314
90 % 32 117 331
70 % 33 124 341
50 % 33 134 357
40 % 33 142 326
30 % 33 145 331
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 % 31 112 233
95 % 31 112 327 Flexibility: Low
Max RMSD: 1.0, Avg RMSD: 0.5
PDBFlex
90 % 31 112 346
70 % 31 112 379
50 % 31 114 440
40 % 31 114 472
30 % 31 114 472
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 % 16 61 565
95 % 16 61 781 Flexibility: Low
Max RMSD: 3.5, Avg RMSD: 0.8
PDBFlex
90 % 16 61 809
70 % 16 62 835
50 % 17 69 753
40 % 17 69 786
30 % 17 69 779
Entity #5 | Chains: E
DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 1 protein, length: 215 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name Structural variation in cluster
100 % 35 143 172
95 % 35 143 233 Flexibility: Low
Max RMSD: 2.1, Avg RMSD: 0.7
PDBFlex
90 % 35 143 248
70 % 36 148 271
50 % 36 150 290
40 % 36 160 286
30 % 36 160 293
Entity #6 | Chains: F
DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 2 protein, length: 155 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name Structural variation in cluster
100 % 33 137 187
95 % 33 137 248 Flexibility: Low
Max RMSD: 1.4, Avg RMSD: 0.6
PDBFlex
90 % 33 137 263
70 % 33 137 294
50 % 34 155 279
40 % 34 155 298
30 % 34 155 309
Entity #7 | Chains: G
RPB7, 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 % 17 64 524
95 % 17 64 715 Flexibility: Low
Max RMSD: 4.4, Avg RMSD: 0.8
PDBFlex
90 % 17 64 745
70 % 17 64 797
50 % 19 82 567
40 % 19 82 605
30 % 19 82 595
Entity #8 | Chains: H
DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 3 protein, length: 146 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name Structural variation in cluster
100 % 33 142 174
95 % 34 143 234 Flexibility: Low
Max RMSD: 1.9, Avg RMSD: 0.9
PDBFlex
90 % 34 143 249
70 % 34 143 281
50 % 35 148 298
40 % 35 148 314
30 % 35 161 292
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 % 32 116 228
95 % 32 116 321 Flexibility: Low
Max RMSD: 2.9, Avg RMSD: 1.0
PDBFlex
90 % 32 116 339
70 % 33 121 356
50 % 33 123 406
40 % 33 123 437
30 % 33 126 427

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.