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 % 17 115 226
95 % 17 115 318 Flexibility: Low
Max RMSD: 6.8, Avg RMSD: 1.6
PDBFlex
90 % 17 115 335
70 % 18 120 352
50 % 18 131 363
40 % 18 131 387
30 % 18 131 395
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 % 19 142 173
95 % 19 142 233 Flexibility: No
Max RMSD: 1.1, Avg RMSD: 0.5
PDBFlex
90 % 19 142 248
70 % 20 158 251
50 % 20 166 247
40 % 20 166 264
30 % 20 166 271
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 % 17 117 221
95 % 17 117 311 Flexibility: No
Max RMSD: 1.1, Avg RMSD: 0.5
PDBFlex
90 % 17 117 328
70 % 17 117 365
50 % 18 122 410
40 % 18 124 426
30 % 18 124 427
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 % 18 138 180
95 % 18 138 242 Flexibility: Low
Max RMSD: 2.0, Avg RMSD: 1.0
PDBFlex
90 % 18 138 256
70 % 18 138 286
50 % 19 143 309
40 % 19 143 321
30 % 19 143 334
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 28095
95 % 1 3 23310 Flexibility: Low
Max RMSD: 0.6, Avg RMSD: 0.5
PDBFlex
90 % 1 3 22555
70 % 1 3 20626
50 % 1 3 17889
40 % 1 3 15946
30 % 1 3 13637
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
100 % 17 116 223
95 % 17 117 308
90 % 17 117 324
70 % 18 124 332
50 % 18 133 349
40 % 18 141 322
30 % 18 144 328
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 % 16 112 230
95 % 16 112 322 Flexibility: Low
Max RMSD: 1.0, Avg RMSD: 0.5
PDBFlex
90 % 16 112 341
70 % 16 112 376
50 % 16 114 437
40 % 16 114 465
30 % 16 114 467
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 % 8 61 562
95 % 8 61 780 Flexibility: Low
Max RMSD: 3.5, Avg RMSD: 0.7
PDBFlex
90 % 8 61 808
70 % 8 62 832
50 % 9 69 749
40 % 9 69 778
30 % 9 69 773
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 % 20 143 170
95 % 20 143 231 Flexibility: Low
Max RMSD: 2.1, Avg RMSD: 0.7
PDBFlex
90 % 20 143 246
70 % 21 148 268
50 % 21 150 289
40 % 21 159 285
30 % 21 159 293
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 % 18 137 183
95 % 18 137 245 Flexibility: Low
Max RMSD: 1.4, Avg RMSD: 0.6
PDBFlex
90 % 18 137 259
70 % 18 137 290
50 % 19 154 281
40 % 19 154 297
30 % 19 154 308
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 % 9 64 514
95 % 9 64 706 Flexibility: Low
Max RMSD: 4.4, Avg RMSD: 0.6
PDBFlex
90 % 9 64 735
70 % 9 64 788
50 % 11 81 569
40 % 11 81 609
30 % 11 81 604
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 63749
95 % 19 143 232 Flexibility: Low
Max RMSD: 1.9, Avg RMSD: 0.9
PDBFlex
90 % 19 143 247
70 % 19 143 277
50 % 20 148 293
40 % 20 148 307
30 % 20 160 292
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 % 17 116 225
95 % 17 116 317 Flexibility: Low
Max RMSD: 2.9, Avg RMSD: 1.0
PDBFlex
90 % 17 116 334
70 % 18 121 351
50 % 18 123 402
40 % 18 123 431
30 % 18 126 420

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.


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 3PO2 4 D DNA-directed RNA polymerase II subunit RPB4 4932 2.7.7.6 | Details
2 3PO3 4 D DNA-directed RNA polymerase II subunit RPB4 4932 2.7.7.6 | Details
3 4A3E 4 D DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB4 4932
4 4A3D 4 D DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB4 4932
5 5IP7 4 D DNA-directed RNA polymerase II subunit RPB4 4932
6 4A3F 4 D DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB4 4932
7 4A93 4 D DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB4 4932
8 4BY7 4 D DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB4 4932
9 4A3C 4 D DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB4 4932
10 4A3K 4 D DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB4 4932
11 4A3L 4 D DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB4 4932
12 4BXX 4 D DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB4 4932
13 4A3G 4 D DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB4 4932
14 4A3B 4 D DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB4 4932
15 4BBR 4 D DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB4 4932
16 4A3J 4 D DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB4 4932
17 4A3I 4 D DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB4 4932
18 4BY1 4 D DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB4 4932
19 4A3M 4 D DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB4 4932
20 5IP9 4 D DNA-directed RNA polymerase II subunit RPB4 4932
21 4BBS 4 D DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB4 4932
22 3HOU 4 D, P DNA-directed RNA polymerase II subunit RPB4 4932 2.7.7.6 | Details
23 3HOY 4 D DNA-directed RNA polymerase II subunit RPB4 4932 2.7.7.6 | Details
24 3HOV 4 D DNA-directed RNA polymerase II subunit RPB4 4932 2.7.7.6 | Details
25 5C3E 4 D DNA-directed RNA polymerase II subunit RPB4 4932
26 3HOZ 4 D DNA-directed RNA polymerase II subunit RPB4 4932 2.7.7.6 | Details
27 3HOW 4 D DNA-directed RNA polymerase II subunit RPB4 4932 2.7.7.6 | Details
28 3HOX 4 D DNA-directed RNA polymerase II subunit RPB4 4932 2.7.7.6 | Details
29 2R92 6 D DNA-directed RNA polymerase II subunit RPB4 4932 2.7.7.6 | Details
30 2R7Z 7 D DNA-directed RNA polymerase II subunit RPB4 4932 2.7.7.6 | Details
31 3I4M 4 D DNA-directed RNA polymerase II subunit RPB4 4932
32 3H3V 4 E DNA-directed RNA polymerase II subunit RPB4 4932 2.7.7.6 | Details
33 5U5Q 4 D DNA-directed RNA polymerase II subunit RPB4 4932
34 5C4X 4 D DNA-directed RNA polymerase II subunit RPB4 4932
35 2VUM 4 D DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB4 4932 2.7.7.6 | Details
36 5C44 4 D DNA-directed RNA polymerase II subunit RPB4 4932
37 2R93 5 D DNA-directed RNA polymerase II subunit RPB4 4932 2.7.7.6 | Details
38 3I4N 4 D DNA-directed RNA polymerase II subunit RPB4 4932
39 4BXZ 4 D DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB4 4932 2.7.7.6 | Details
40 5C4A 4 D DNA-directed RNA polymerase II subunit RPB4 4932
41 3K1F 4 D DNA-directed RNA polymerase II subunit RPB4 4932 2.7.7.6 | Details
42 2JA7 7 D, P DNA-DIRECTED RNA POLYMERASE II 32KDA POLYPEPTIDE 4932 2.7.7.6 | Details
43 1Y1W 7 D DNA-directed RNA polymerase II 32 kDa polypeptide 4932 2.7.7.6 | Details
44 3QT1 4 D DNA-directed RNA polymerase II subunit RPB4 4932 2.7.7.6 | Details
45 2JA8 4 D DNA-DIRECTED RNA POLYMERASE II 32KDA POLYPEPTIDE 4932 2.7.7.6 | Details
46 2JA5 4 D DNA-directed RNA polymerase II subunit RPB4 4932
47 2B63 5 D DNA-directed RNA polymerase II 32 kDa polypeptide 4932 2.7.7.6 | Details
48 1Y1V 4 D DNA-directed RNA polymerase II 32 kDa polypeptide 4932 2.7.7.6 | Details
49 3FKI 4 D DNA-directed RNA polymerase II subunit RPB4 4932
50 1Y1Y 6 D DNA-directed RNA polymerase II 32 kDa polypeptide 4932 2.7.7.6 | Details
51 2JA6 4 D DNA-DIRECTED RNA POLYMERASE II 32KDA POLYPEPTIDE 4932 2.7.7.6 | Details
52 1Y77 7 D DNA-directed RNA polymerase II 32 kDa polypeptide 4932 2.7.7.6 | Details
53 2B8K 4 D DNA-directed RNA polymerase II 32 kDa polypeptide 4932 2.7.7.6 | Details
54 5SVA 4 D DNA-directed RNA polymerase II subunit RPB4 4932
55 5FYW 4 D DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB4 4932
56 5FZ5 4 D DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB4 4932
57 4V1N 4 D DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB4 4932
58 4V1O 4 D DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB4 4932
59 3J1N 4 D DNA-directed RNA polymerase II subunit RPB4 4932
60 3J0K 4 D DNA-directed RNA polymerase II 32 kDa polypeptide 9606 2.7.7.6 | Details
61 1NT9 4 D YEAST DNA-DIRECTED RNA POLYMERASE II 32 KD POLYPEPTIDE Numbering of resiudes D10-D24 is arbitrary 4932 2.7.7.6 | Details