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 % 18 123 229
95 % 18 123 319 Flexibility: Low
Max RMSD: 5.3, Avg RMSD: 1.6
PDBFlex
90 % 18 123 333
70 % 19 128 356
50 % 19 141 380
40 % 19 141 401
30 % 19 141 401
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 % 20 158 173
95 % 20 158 234 Flexibility: No
Max RMSD: 1.1, Avg RMSD: 0.5
PDBFlex
90 % 20 158 246
70 % 21 176 229
50 % 21 184 231
40 % 21 184 250
30 % 21 184 260
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 % 18 125 224
95 % 18 125 313 Flexibility: No
Max RMSD: 1.0, Avg RMSD: 0.5
PDBFlex
90 % 18 125 326
70 % 18 125 374
50 % 19 130 421
40 % 19 132 428
30 % 19 132 429
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 % 19 154 177
95 % 19 154 239 Flexibility: Low
Max RMSD: 2.0, Avg RMSD: 1.0
PDBFlex
90 % 19 154 251
70 % 19 154 283
50 % 20 159 293
40 % 20 159 315
30 % 20 159 322
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 29814
95 % 1 3 24709 Flexibility: Low
Max RMSD: 0.6, Avg RMSD: 0.5
PDBFlex
90 % 1 3 23872
70 % 1 3 21720
50 % 1 3 18772
40 % 1 3 16711
30 % 1 3 14290
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 % 18 124 225
95 % 18 125 312 Flexibility: Low
Max RMSD: 3.3, Avg RMSD: 1.3
PDBFlex
90 % 18 125 324
70 % 19 132 337
50 % 19 143 372
40 % 19 151 340
30 % 19 162 306
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 % 17 120 237
95 % 17 120 325 Flexibility: Low
Max RMSD: 1.0, Avg RMSD: 0.5
PDBFlex
90 % 17 120 341
70 % 17 120 383
50 % 17 122 442
40 % 17 122 468
30 % 17 122 461
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 % 9 64 565
95 % 9 64 761 Flexibility: Low
Max RMSD: 3.5, Avg RMSD: 0.7
PDBFlex
90 % 9 64 790
70 % 9 65 829
50 % 10 72 750
40 % 10 72 786
30 % 10 72 781
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 % 21 159 170
95 % 21 159 232 Flexibility: Low
Max RMSD: 2.1, Avg RMSD: 0.7
PDBFlex
90 % 21 159 244
70 % 22 164 255
50 % 22 166 273
40 % 22 177 267
30 % 22 177 277
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 % 19 153 179
95 % 19 153 243 Flexibility: Low
Max RMSD: 1.4, Avg RMSD: 0.6
PDBFlex
90 % 19 153 255
70 % 19 153 288
50 % 20 172 263
40 % 20 172 274
30 % 20 172 286
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 % 10 67 506
95 % 10 67 694 Flexibility: Low
Max RMSD: 4.2, Avg RMSD: 0.7
PDBFlex
90 % 10 67 724
70 % 10 67 772
50 % 12 86 568
40 % 12 86 603
30 % 12 86 598
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 67290
95 % 20 159 233 Flexibility: Low
Max RMSD: 1.9, Avg RMSD: 1.0
PDBFlex
90 % 20 159 245
70 % 20 159 274
50 % 21 164 281
40 % 21 164 297
30 % 21 178 276
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 % 18 124 228
95 % 18 124 317 Flexibility: Low
Max RMSD: 2.9, Avg RMSD: 1.0
PDBFlex
90 % 18 124 331
70 % 19 129 354
50 % 19 131 413
40 % 19 131 432
30 % 19 142 400

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


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 5OT2 4 D DNA-directed RNA polymerase II subunit RPB4 4932
5 4A3D 4 D DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB4 4932
6 5IP7 4 D DNA-directed RNA polymerase II subunit RPB4 4932
7 4A3F 4 D DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB4 4932
8 4A93 4 D DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB4 4932
9 4BY7 4 D DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB4 4932
10 4A3C 4 D DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB4 4932
11 4A3K 4 D DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB4 4932
12 4A3L 4 D DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB4 4932
13 4BXX 4 D DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB4 4932
14 4A3G 4 D DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB4 4932
15 4A3B 4 D DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB4 4932
16 4BBR 4 D DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB4 4932
17 4A3J 4 D DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB4 4932
18 4A3I 4 D DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB4 4932
19 4BY1 4 D DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB4 4932
20 4A3M 4 D DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB4 4932
21 5IP9 4 D DNA-directed RNA polymerase II subunit RPB4 4932
22 4BBS 4 D DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB4 4932
23 3HOU 4 D, P DNA-directed RNA polymerase II subunit RPB4 4932 2.7.7.6 | Details
24 3HOY 4 D DNA-directed RNA polymerase II subunit RPB4 4932 2.7.7.6 | Details
25 3HOV 4 D DNA-directed RNA polymerase II subunit RPB4 4932 2.7.7.6 | Details
26 5C3E 4 D DNA-directed RNA polymerase II subunit RPB4 4932
27 3HOZ 4 D DNA-directed RNA polymerase II subunit RPB4 4932 2.7.7.6 | Details
28 3HOW 4 D DNA-directed RNA polymerase II subunit RPB4 4932 2.7.7.6 | Details
29 3HOX 4 D DNA-directed RNA polymerase II subunit RPB4 4932 2.7.7.6 | Details
30 2R92 6 D DNA-directed RNA polymerase II subunit RPB4 4932 2.7.7.6 | Details
31 2R7Z 7 D DNA-directed RNA polymerase II subunit RPB4 4932 2.7.7.6 | Details
32 3I4M 4 D DNA-directed RNA polymerase II subunit RPB4 4932
33 3H3V 4 E DNA-directed RNA polymerase II subunit RPB4 4932 2.7.7.6 | Details
34 5U5Q 4 D DNA-directed RNA polymerase II subunit RPB4 4932
35 5C4X 4 D DNA-directed RNA polymerase II subunit RPB4 4932
36 2VUM 4 D DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB4 4932 2.7.7.6 | Details
37 5C44 4 D DNA-directed RNA polymerase II subunit RPB4 4932
38 2R93 5 D DNA-directed RNA polymerase II subunit RPB4 4932 2.7.7.6 | Details
39 3I4N 4 D DNA-directed RNA polymerase II subunit RPB4 4932
40 4BXZ 4 D DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB4 4932 2.7.7.6 | Details
41 5C4A 4 D DNA-directed RNA polymerase II subunit RPB4 4932
42 3K1F 4 D DNA-directed RNA polymerase II subunit RPB4 4932 2.7.7.6 | Details
43 2JA7 7 D, P DNA-DIRECTED RNA POLYMERASE II 32KDA POLYPEPTIDE 4932 2.7.7.6 | Details
44 1Y1W 7 D DNA-directed RNA polymerase II 32 kDa polypeptide 4932 2.7.7.6 | Details
45 3QT1 4 D DNA-directed RNA polymerase II subunit RPB4 4932 2.7.7.6 | Details
46 2JA8 4 D DNA-DIRECTED RNA POLYMERASE II 32KDA POLYPEPTIDE 4932 2.7.7.6 | Details
47 2JA5 4 D DNA-directed RNA polymerase II subunit RPB4 4932
48 2B63 5 D DNA-directed RNA polymerase II 32 kDa polypeptide 4932 2.7.7.6 | Details
49 1Y1V 4 D DNA-directed RNA polymerase II 32 kDa polypeptide 4932 2.7.7.6 | Details
50 3FKI 4 D DNA-directed RNA polymerase II subunit RPB4 4932
51 1Y1Y 6 D DNA-directed RNA polymerase II 32 kDa polypeptide 4932 2.7.7.6 | Details
52 2JA6 4 D DNA-DIRECTED RNA POLYMERASE II 32KDA POLYPEPTIDE 4932 2.7.7.6 | Details
53 1Y77 7 D DNA-directed RNA polymerase II 32 kDa polypeptide 4932 2.7.7.6 | Details
54 2B8K 4 D DNA-directed RNA polymerase II 32 kDa polypeptide 4932 2.7.7.6 | Details
55 5VVS 4 D DNA-directed RNA polymerase II subunit RPB4 4932
56 5VVR 4 D DNA-directed RNA polymerase II subunit RPB4 4932
57 5SVA 4 D DNA-directed RNA polymerase II subunit RPB4 4932
58 5FYW 4 D DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB4 4932
59 5FZ5 4 D DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB4 4932
60 4V1N 4 D DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB4 4932
61 4V1O 4 D DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB4 4932
62 3J1N 4 D DNA-directed RNA polymerase II subunit RPB4 4932
63 3J0K 4 D DNA-directed RNA polymerase II 32 kDa polypeptide 9606 2.7.7.6 | Details
64 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