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 % 18 118 231
95 % 18 118 321 Flexibility: Low
Max RMSD: 5.3, Avg RMSD: 1.6
PDBFlex
90 % 18 118 337
70 % 19 123 360
50 % 19 135 381
40 % 19 135 404
30 % 19 135 402
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 % 20 145 178
95 % 20 145 240 Flexibility: No
Max RMSD: 1.1, Avg RMSD: 0.5
PDBFlex
90 % 20 145 255
70 % 21 162 252
50 % 21 170 247
40 % 21 170 268
30 % 21 170 272
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 % 18 120 225
95 % 18 120 316 Flexibility: No
Max RMSD: 1.0, Avg RMSD: 0.5
PDBFlex
90 % 18 120 331
70 % 18 120 372
50 % 19 125 419
40 % 19 127 433
30 % 19 127 437
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 % 19 141 183
95 % 19 141 246 Flexibility: Low
Max RMSD: 2.0, Avg RMSD: 1.0
PDBFlex
90 % 19 141 262
70 % 19 141 299
50 % 20 146 321
40 % 20 146 341
30 % 20 146 349
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 28951
95 % 1 3 24043 Flexibility: Low
Max RMSD: 0.6, Avg RMSD: 0.5
PDBFlex
90 % 1 3 23246
70 % 1 3 21174
50 % 1 3 18322
40 % 1 3 16325
30 % 1 3 13960
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 % 18 119 226
95 % 18 120 314 Flexibility: Low
Max RMSD: 3.3, Avg RMSD: 1.3
PDBFlex
90 % 18 120 328
70 % 19 127 342
50 % 19 137 373
40 % 19 145 336
30 % 19 148 334
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 % 17 115 234
95 % 17 115 331 Flexibility: Low
Max RMSD: 1.0, Avg RMSD: 0.5
PDBFlex
90 % 17 115 349
70 % 17 115 382
50 % 17 117 445
40 % 17 117 473
30 % 17 117 469
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 64 550
95 % 9 64 744 Flexibility: Low
Max RMSD: 3.5, Avg RMSD: 0.7
PDBFlex
90 % 9 64 774
70 % 9 65 808
50 % 10 72 731
40 % 10 72 765
30 % 10 72 758
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 % 21 146 176
95 % 21 146 237 Flexibility: Low
Max RMSD: 2.1, Avg RMSD: 0.7
PDBFlex
90 % 21 146 251
70 % 22 151 279
50 % 22 153 293
40 % 22 163 290
30 % 22 163 295
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 % 19 140 185
95 % 19 140 248 Flexibility: Low
Max RMSD: 1.4, Avg RMSD: 0.6
PDBFlex
90 % 19 140 263
70 % 19 140 300
50 % 20 158 279
40 % 20 158 296
30 % 20 158 305
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 67 493
95 % 10 67 685 Flexibility: Low
Max RMSD: 4.2, Avg RMSD: 0.7
PDBFlex
90 % 10 67 715
70 % 10 67 760
50 % 12 85 564
40 % 12 85 600
30 % 12 85 591
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 65539
95 % 20 146 238 Flexibility: Low
Max RMSD: 1.9, Avg RMSD: 1.0
PDBFlex
90 % 20 146 252
70 % 20 146 287
50 % 21 151 307
40 % 21 151 322
30 % 21 164 292
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 % 18 119 230
95 % 18 119 319 Flexibility: Low
Max RMSD: 2.9, Avg RMSD: 1.0
PDBFlex
90 % 18 119 335
70 % 19 124 359
50 % 19 126 408
40 % 19 126 439
30 % 19 129 429

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 1PQV 4 D DNA-directed RNA polymerase II 32 kDa polypeptide 4932 2.7.7.6 | Details
65 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