Sequence Similarity Clusters for the Entities in PDB 4A3D

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 % 11 132 258
95 % 11 132 345 Flexibility: Low
Max RMSD: 6.8, Avg RMSD: 1.6
PDBFlex
90 % 11 132 358
70 % 12 151 341
50 % 12 153 399
40 % 12 153 423
30 % 12 153 438
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 % 13 177 183
95 % 13 177 241 Flexibility: No
Max RMSD: 1.1, Avg RMSD: 0.5
PDBFlex
90 % 13 177 251
70 % 14 213 237
50 % 14 213 248
40 % 14 213 264
30 % 14 213 281
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 % 11 134 242
95 % 11 134 331 Flexibility: No
Max RMSD: 1.1, Avg RMSD: 0.5
PDBFlex
90 % 11 134 343
70 % 11 134 384
50 % 12 153 404
40 % 12 155 418
30 % 12 155 433
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 % 13 173 187
95 % 13 173 244 Flexibility: Low
Max RMSD: 2.0, Avg RMSD: 1.0
PDBFlex
90 % 13 173 256
70 % 13 173 296
50 % 14 192 312
40 % 14 192 329
30 % 14 192 345
Entity #13 | Chains: N
NON TEMPLATE DNA 5'-D(*TP*AP*AP*GP*TP*AP*CP*TP*TP *GP*AP*GP*CP*TP)-3' dna, length: 14 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
Entity #14 | Chains: P
TRANSCRIPT RNA 5'-R(*CP*CP*AP*GP*GP*AP)-3' rna, length: 6 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
Entity #15 | Chains: T
TEMPLATE DNA 5'-D(*AP*GP*CP*TP*CP*AP*AP*GP*TP*AP*CP *TP*TP*TP*TP*TP*CP*CP*TP*BRUP*GP*GP*TP*CP*AP*TP*TP)-3' dna, length: 26 (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 % 11 133 249
95 % 11 134 329 Flexibility: Low
Max RMSD: 3.3, Avg RMSD: 1.2
PDBFlex
90 % 11 134 345
70 % 12 155 333
50 % 12 170 362
40 % 12 178 355
30 % 12 193 337
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 % 11 129 269
95 % 11 129 360 Flexibility: Low
Max RMSD: 1.0, Avg RMSD: 0.5
PDBFlex
90 % 11 129 375
70 % 11 129 413
50 % 11 129 462
40 % 11 131 484
30 % 11 131 515
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 % 5 70 588
95 % 5 70 798 Flexibility: Low
Max RMSD: 3.5, Avg RMSD: 0.8
PDBFlex
90 % 5 70 841
70 % 5 71 867
50 % 5 71 904
40 % 5 71 947
30 % 5 71 986
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 % 14 178 181
95 % 14 178 239 Flexibility: Low
Max RMSD: 2.1, Avg RMSD: 0.7
PDBFlex
90 % 14 178 248
70 % 15 197 259
50 % 15 199 287
40 % 15 214 256
30 % 15 214 272
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 % 13 172 188
95 % 13 172 245 Flexibility: Low
Max RMSD: 1.4, Avg RMSD: 0.6
PDBFlex
90 % 13 172 257
70 % 13 172 298
50 % 14 193 305
40 % 14 193 322
30 % 14 193 335
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 % 6 73 556
95 % 6 73 753 Flexibility: Low
Max RMSD: 4.4, Avg RMSD: 0.7
PDBFlex
90 % 6 73 798
70 % 6 73 831
50 % 8 110 507
40 % 8 110 542
30 % 8 110 565
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 % 13 177 182
95 % 13 178 238 Flexibility: Low
Max RMSD: 1.9, Avg RMSD: 1.0
PDBFlex
90 % 13 178 247
70 % 13 178 285
50 % 14 197 298
40 % 14 197 312
30 % 14 213 287
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 % 11 133 250
95 % 11 133 336 Flexibility: Low
Max RMSD: 2.9, Avg RMSD: 1.0
PDBFlex
90 % 11 133 352
70 % 12 152 339
50 % 12 154 395
40 % 12 154 420
30 % 12 169 397

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