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 69 539
95 % 55 69 674 Flexibility: Low
Max RMSD: 4.4, Avg RMSD: 0.7
PDBFlex
90 % 55 69 699
70 % 55 69 741
50 % 59 88 561
40 % 59 88 602
30 % 59 88 605
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 % 114 162 184
95 % 115 163 231 Flexibility: Low
Max RMSD: 1.9, Avg RMSD: 0.9
PDBFlex
90 % 115 163 240
70 % 115 163 271
50 % 117 168 282
40 % 117 168 314
30 % 118 182 288
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 % 109 128 234
95 % 109 128 307 Flexibility: Low
Max RMSD: 2.9, Avg RMSD: 1.0
PDBFlex
90 % 109 128 318
70 % 111 133 343
50 % 112 135 404
40 % 112 135 428
30 % 112 146 404
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 % 115 162 183
95 % 115 162 233 Flexibility: No
Max RMSD: 1.1, Avg RMSD: 0.5
PDBFlex
90 % 115 162 241
70 % 118 180 230
50 % 126 188 229
40 % 126 188 254
30 % 126 188 274
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 Structural variation in cluster
100 % 110 129 232
95 % 110 129 300 Flexibility: No
Max RMSD: 1.1, Avg RMSD: 0.5
PDBFlex
90 % 110 129 312
70 % 110 129 361
50 % 112 134 407
40 % 113 136 425
30 % 113 136 426
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 Structural variation in cluster
100 % 113 158 185
95 % 113 158 241 Flexibility: Low
Max RMSD: 2.0, Avg RMSD: 1.0
PDBFlex
90 % 113 158 247
70 % 113 158 278
50 % 115 163 296
40 % 115 163 327
30 % 115 163 334
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 % 110 127 236
95 % 110 127 312 Flexibility: Low
Max RMSD: 6.8, Avg RMSD: 1.6
PDBFlex
90 % 110 127 324
70 % 112 132 347
50 % 113 145 379
40 % 113 145 407
30 % 113 145 405
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 % 110 129 233
95 % 110 129 306 Flexibility: Low
Max RMSD: 3.3, Avg RMSD: 1.2
PDBFlex
90 % 110 129 317
70 % 113 136 335
50 % 113 147 373
40 % 121 155 353
30 % 231 308 143
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 % 108 124 244
95 % 108 124 321 Flexibility: Low
Max RMSD: 1.0, Avg RMSD: 0.5
PDBFlex
90 % 108 124 332
70 % 108 124 376
50 % 108 124 444
40 % 108 124 475
30 % 108 124 480
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 66 601
95 % 53 66 738 Flexibility: Low
Max RMSD: 3.5, Avg RMSD: 0.8
PDBFlex
90 % 53 66 761
70 % 54 69 768
50 % 56 74 748
40 % 56 74 779
30 % 56 74 782
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 % 116 163 182
95 % 116 163 232 Flexibility: Low
Max RMSD: 2.1, Avg RMSD: 0.7
PDBFlex
90 % 116 163 238
70 % 118 168 254
50 % 119 170 271
40 % 119 181 278
30 % 119 181 294
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 % 113 157 186
95 % 113 157 242 Flexibility: Low
Max RMSD: 1.4, Avg RMSD: 0.6
PDBFlex
90 % 113 157 248
70 % 113 157 281
50 % 116 176 262
40 % 116 176 288
30 % 116 176 298

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