Sequence Similarity Clusters for the Entities in PDB 4BY7

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 % 18 118 236
95 % 18 118 325 Flexibility: Low
Max RMSD: 5.3, Avg RMSD: 1.6
PDBFlex
90 % 18 118 343
70 % 19 123 368
50 % 19 135 386
40 % 19 135 416
30 % 19 135 414
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 % 20 153 176
95 % 20 153 239 Flexibility: No
Max RMSD: 1.1, Avg RMSD: 0.5
PDBFlex
90 % 20 153 251
70 % 21 170 246
50 % 21 178 236
40 % 21 178 255
30 % 21 178 264
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 % 18 120 231
95 % 18 120 320 Flexibility: No
Max RMSD: 1.0, Avg RMSD: 0.5
PDBFlex
90 % 18 120 337
70 % 18 120 379
50 % 19 125 429
40 % 19 127 442
30 % 19 127 444
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 % 19 149 181
95 % 19 149 242 Flexibility: Low
Max RMSD: 2.0, Avg RMSD: 1.0
PDBFlex
90 % 19 149 255
70 % 19 149 291
50 % 20 154 306
40 % 20 154 325
30 % 20 154 329
Entity #13 | Chains: N
, 5'-D(*DAP*AP*AP*GP*TP*AP*CP*TP*TP*GP*AP*GP*CP*DTP)-3' dna, length: 14 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
Entity #14 | 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 #15 | Chains: T
5'-D(*DAP*GP*CP*TP*CP*AP*AP*GP*TP*AP*CP*TP*TP*DAP *TP*TP*CP*CP*BP*GP*GP*TP*CP*AP*TP*T)-3' dna, length: 26 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
Entity #16 | Chains: X
TRANSCRIPTION FACTOR BYE1 protein, length: 146 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name Structural variation in cluster
100 % 1 3 29458
95 % 1 3 24416 Flexibility: Low
Max RMSD: 0.6, Avg RMSD: 0.5
PDBFlex
90 % 1 3 23595
70 % 1 3 21481
50 % 1 3 18581
40 % 1 3 16545
30 % 1 3 14146
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 % 18 119 232
95 % 18 120 319 Flexibility: Low
Max RMSD: 3.3, Avg RMSD: 1.3
PDBFlex
90 % 18 120 335
70 % 19 127 351
50 % 19 137 377
40 % 19 145 348
30 % 19 156 317
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 % 17 115 238
95 % 17 115 333 Flexibility: Low
Max RMSD: 1.0, Avg RMSD: 0.5
PDBFlex
90 % 17 115 353
70 % 17 115 389
50 % 17 117 449
40 % 17 117 479
30 % 17 117 471
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 % 9 64 557
95 % 9 64 753 Flexibility: Low
Max RMSD: 3.5, Avg RMSD: 0.7
PDBFlex
90 % 9 64 783
70 % 9 65 817
50 % 10 72 741
40 % 10 72 778
30 % 10 72 771
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 % 21 154 172
95 % 21 154 234 Flexibility: Low
Max RMSD: 2.1, Avg RMSD: 0.7
PDBFlex
90 % 21 154 246
70 % 22 159 268
50 % 22 161 285
40 % 22 171 274
30 % 22 171 284
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 % 19 148 182
95 % 19 148 245 Flexibility: Low
Max RMSD: 1.4, Avg RMSD: 0.6
PDBFlex
90 % 19 148 258
70 % 19 148 293
50 % 20 166 274
40 % 20 166 288
30 % 20 166 299
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 % 10 67 500
95 % 10 67 693 Flexibility: Low
Max RMSD: 4.2, Avg RMSD: 0.7
PDBFlex
90 % 10 67 724
70 % 10 67 765
50 % 12 85 571
40 % 12 85 608
30 % 12 85 598
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 % 1 1 66524
95 % 20 154 235 Flexibility: Low
Max RMSD: 1.9, Avg RMSD: 1.0
PDBFlex
90 % 20 154 247
70 % 20 154 281
50 % 21 159 289
40 % 21 159 309
30 % 21 172 282
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 % 18 119 235
95 % 18 119 322 Flexibility: Low
Max RMSD: 2.9, Avg RMSD: 1.0
PDBFlex
90 % 18 119 340
70 % 19 124 367
50 % 19 126 419
40 % 19 126 447
30 % 19 137 405

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


ACTION - (A) Select for download / view details OR (B) Select two chains for comparison
Rank PDB ID Entity ID Chains Description Details Taxonomy EC Number
1 4BY7 16 X TRANSCRIPTION FACTOR BYE1 TFIIS-LIKE DOMAIN 4932
2 4BXX 16 X TRANSCRIPTION FACTOR BYE1 RESIDUES 225-370 4932
3 4BY1 16 X TRANSCRIPTION FACTOR BYE1 RESIDUES 225-370 4932