Sequence Similarity Clusters for the Entities in PDB 2JA7

Entity #1 | Chains: 1,4
5'-D(*TP*AP*AP*GP*TP*AP*CP*TP*TP*GP *AP*GP*CP*T)-3' dna, length: 14 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
Entity #10 | Chains: G,S
DNA-DIRECTED RNA POLYMERASE II 19KDA POLYPEPTIDE protein, length: 171 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name Structural variation in cluster
100 % 45 69 537
95 % 45 69 672 Flexibility: Low
Max RMSD: 4.2, Avg RMSD: 0.7
PDBFlex
90 % 45 69 697
70 % 45 69 739
50 % 47 88 557
40 % 47 88 599
30 % 47 88 605
Entity #11 | Chains: H,T
DNA-DIRECTED RNA POLYMERASES I, II, AND III 14.5 KDA POLYPEPTIDE protein, length: 146 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name Structural variation in cluster
100 % 91 160 183
95 % 92 161 232 Flexibility: Low
Max RMSD: 1.9, Avg RMSD: 1.0
PDBFlex
90 % 92 161 240
70 % 92 161 270
50 % 93 166 279
40 % 93 166 311
30 % 93 180 291
Entity #12 | Chains: I,U
DNA-DIRECTED RNA POLYMERASE II SUBUNIT 9 protein, length: 122 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name Structural variation in cluster
100 % 88 126 235
95 % 88 126 313 Flexibility: Low
Max RMSD: 2.9, Avg RMSD: 1.0
PDBFlex
90 % 88 126 323
70 % 89 131 348
50 % 89 133 401
40 % 89 133 431
30 % 89 144 403
Entity #13 | Chains: J,V
DNA-DIRECTED RNA POLYMERASES I/II/III SUBUNIT 10 protein, length: 70 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name Structural variation in cluster
100 % 92 160 182
95 % 92 160 234 Flexibility: No
Max RMSD: 1.1, Avg RMSD: 0.5
PDBFlex
90 % 92 160 241
70 % 93 178 234
50 % 98 186 229
40 % 98 186 256
30 % 98 186 275
Entity #14 | Chains: K,W
DNA-DIRECTED RNA POLYMERASE II 13.6 KDA POLYPEPTIDE protein, length: 120 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name Structural variation in cluster
100 % 88 127 230
95 % 88 127 308 Flexibility: No
Max RMSD: 1.0, Avg RMSD: 0.5
PDBFlex
90 % 88 127 318
70 % 88 127 369
50 % 89 132 411
40 % 89 134 427
30 % 89 134 435
Entity #15 | Chains: L,X
DNA-DIRECTED RNA POLYMERASES I, II, AND III 7.7 KDA POLYPEPTIDE protein, length: 70 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name Structural variation in cluster
100 % 90 156 187
95 % 90 156 240 Flexibility: Low
Max RMSD: 2.0, Avg RMSD: 1.0
PDBFlex
90 % 90 156 249
70 % 90 156 280
50 % 91 161 294
40 % 91 161 322
30 % 91 161 329
Entity #2 | Chains: 2,5
5'-D(*AP*GP*CP*TP*CP*AP*AP*GP*TP*AP *CP*TP*TP*TP*TTP*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 #3 | Chains: 3,6
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 #4 | Chains: A,M
DNA-DIRECTED RNA POLYMERASE II LARGEST SUBUNIT protein, length: 1733 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name Structural variation in cluster
100 % 88 125 241
95 % 88 125 319 Flexibility: Low
Max RMSD: 5.3, Avg RMSD: 1.6
PDBFlex
90 % 88 125 328
70 % 89 130 352
50 % 89 143 376
40 % 89 143 407
30 % 89 143 407
Entity #5 | Chains: B,N
DNA-DIRECTED RNA POLYMERASE II 140 KDA POLYPEPTIDE protein, length: 1224 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name Structural variation in cluster
100 % 88 127 232
95 % 88 127 309 Flexibility: Low
Max RMSD: 3.3, Avg RMSD: 1.3
PDBFlex
90 % 88 127 319
70 % 89 134 334
50 % 89 145 371
40 % 94 153 350
30 % 173 306 144
Entity #6 | Chains: C,O
DNA-DIRECTED RNA POLYMERASE II 45KDA POLYPEPTIDE protein, length: 318 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name Structural variation in cluster
100 % 86 122 246
95 % 86 122 326 Flexibility: Low
Max RMSD: 1.0, Avg RMSD: 0.5
PDBFlex
90 % 86 122 339
70 % 86 122 382
50 % 86 122 450
40 % 86 122 479
30 % 86 122 484
Entity #7 | Chains: D,P
DNA-DIRECTED RNA POLYMERASE II 32KDA POLYPEPTIDE protein, length: 221 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name Structural variation in cluster
100 % 43 66 597
95 % 43 66 732 Flexibility: Low
Max RMSD: 3.5, Avg RMSD: 0.7
PDBFlex
90 % 43 66 757
70 % 44 69 764
50 % 45 74 743
40 % 45 74 775
30 % 45 74 779
Entity #8 | Chains: E,Q
DNA-DIRECTED RNA POLYMERASES I, II, AND III 27 KDA POLYPEPTIDE protein, length: 215 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 93 161 181
95 % 93 161 233
90 % 93 161 239
70 % 94 166 253
50 % 94 168 271
40 % 94 179 280
30 % 94 179 295
Entity #9 | Chains: F,R
DNA-DIRECTED RNA POLYMERASES I, II, AND III 23 KDA POLYPEPTIDE protein, length: 155 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name Structural variation in cluster
100 % 90 155 188
95 % 90 155 241 Flexibility: Low
Max RMSD: 1.4, Avg RMSD: 0.6
PDBFlex
90 % 90 155 250
70 % 90 155 281
50 % 91 174 260
40 % 91 174 287
30 % 91 174 301

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