Sequence Similarity Clusters for the Entities in PDB 1Y77

Entity #1 | Chains: T
5'-D(P*AP*GP*TP*AP*CP*TP*TP*AP*CP*T*CP*GP*CP*CP*TP*GP*GP*TP*CP*TP*G)-3' dna, length: 19 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
Entity #10 | Chains: G
DNA-directed RNA polymerase II 19 kDa polypeptide protein, length: 171 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name Structural variation in cluster
100 % 55 67 506
95 % 55 67 694 Flexibility: Low
Max RMSD: 4.2, Avg RMSD: 0.7
PDBFlex
90 % 55 67 724
70 % 55 67 772
50 % 59 86 568
40 % 59 86 603
30 % 59 86 598
Entity #11 | Chains: H
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 % 112 158 172
95 % 113 159 233 Flexibility: Low
Max RMSD: 1.9, Avg RMSD: 1.0
PDBFlex
90 % 113 159 245
70 % 113 159 274
50 % 115 164 281
40 % 115 164 297
30 % 116 178 276
Entity #12 | Chains: I
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 % 107 124 228
95 % 107 124 317 Flexibility: Low
Max RMSD: 2.9, Avg RMSD: 1.0
PDBFlex
90 % 107 124 331
70 % 109 129 354
50 % 110 131 413
40 % 110 131 432
30 % 110 142 400
Entity #13 | Chains: J
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 % 113 158 173
95 % 113 158 234 Flexibility: No
Max RMSD: 1.1, Avg RMSD: 0.5
PDBFlex
90 % 113 158 246
70 % 116 176 229
50 % 124 184 231
40 % 124 184 250
30 % 124 184 260
Entity #14 | Chains: K
DNA-directed RNA polymerase II 13.6 kDa polypeptide protein, length: 120 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 108 125 224
95 % 108 125 313
90 % 108 125 326
70 % 108 125 374
50 % 110 130 421
40 % 111 132 428
30 % 111 132 429
Entity #15 | Chains: L
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
100 % 111 154 177
95 % 111 154 239
90 % 111 154 251
70 % 111 154 283
50 % 113 159 293
40 % 113 159 315
30 % 113 159 322
Entity #2 | Chains: N
5'-D(*AP*AP*GP*TP*AP*CP*T)-3' dna, length: 7 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
Entity #3 | Chains: P
5'-R(*AP*AP*GP*AP*CP*CP*AP*GP*GP*C)-3' rna, length: 10 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
Entity #4 | Chains: A
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 % 108 123 229
95 % 108 123 319 Flexibility: Low
Max RMSD: 5.3, Avg RMSD: 1.6
PDBFlex
90 % 108 123 333
70 % 110 128 356
50 % 111 141 380
40 % 111 141 401
30 % 111 141 401
Entity #5 | Chains: B
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 % 107 124 225
95 % 108 125 312 Flexibility: Low
Max RMSD: 3.3, Avg RMSD: 1.3
PDBFlex
90 % 108 125 324
70 % 111 132 337
50 % 111 143 372
40 % 119 151 340
30 % 119 162 306
Entity #6 | Chains: C
DNA-directed RNA polymerase II 45 kDa polypeptide protein, length: 318 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name Structural variation in cluster
100 % 106 120 237
95 % 106 120 325 Flexibility: Low
Max RMSD: 1.0, Avg RMSD: 0.5
PDBFlex
90 % 106 120 341
70 % 106 120 383
50 % 107 122 442
40 % 107 122 468
30 % 107 122 461
Entity #7 | Chains: D
DNA-directed RNA polymerase II 32 kDa polypeptide protein, length: 221 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name Structural variation in cluster
100 % 53 64 565
95 % 53 64 761 Flexibility: Low
Max RMSD: 3.5, Avg RMSD: 0.7
PDBFlex
90 % 53 64 790
70 % 53 65 829
50 % 56 72 750
40 % 56 72 786
30 % 56 72 781
Entity #8 | Chains: E
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 Structural variation in cluster
100 % 114 159 170
95 % 114 159 232 Flexibility: Low
Max RMSD: 2.1, Avg RMSD: 0.7
PDBFlex
90 % 114 159 244
70 % 116 164 255
50 % 117 166 273
40 % 117 177 267
30 % 117 177 277
Entity #9 | Chains: F
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 % 111 153 179
95 % 111 153 243 Flexibility: Low
Max RMSD: 1.4, Avg RMSD: 0.6
PDBFlex
90 % 111 153 255
70 % 111 153 288
50 % 114 172 263
40 % 114 172 274
30 % 114 172 286

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