Sequence Similarity Clusters for the Entities in PDB 1Y1Y

Entity #1 | Chains: T
5'-D(P*TP*AP*CP*GP*CP*CP*T)-3' dna, length: 7 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
Entity #10 | 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 % 109 162 184
95 % 110 163 231 Flexibility: Low
Max RMSD: 1.9, Avg RMSD: 0.9
PDBFlex
90 % 110 163 240
70 % 110 163 271
50 % 112 168 282
40 % 112 168 314
30 % 113 182 288
Entity #11 | 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 % 104 128 234
95 % 104 128 307 Flexibility: Low
Max RMSD: 2.9, Avg RMSD: 1.0
PDBFlex
90 % 104 128 318
70 % 106 133 343
50 % 107 135 404
40 % 107 135 428
30 % 107 146 404
Entity #12 | 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 % 110 162 183
95 % 110 162 233 Flexibility: No
Max RMSD: 1.1, Avg RMSD: 0.5
PDBFlex
90 % 110 162 241
70 % 113 180 230
50 % 118 188 229
40 % 118 188 254
30 % 118 188 274
Entity #13 | 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 % 105 129 232
95 % 105 129 300 Flexibility: No
Max RMSD: 1.1, Avg RMSD: 0.5
PDBFlex
90 % 105 129 312
70 % 105 129 361
50 % 107 134 407
40 % 108 136 425
30 % 108 136 426
Entity #14 | 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 % 108 158 185
95 % 108 158 241 Flexibility: Low
Max RMSD: 2.0, Avg RMSD: 1.0
PDBFlex
90 % 108 158 247
70 % 108 158 278
50 % 110 163 296
40 % 110 163 327
30 % 110 163 334
Entity #15 | Chains: S
Transcription elongation factor S-II protein, length: 179 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name Structural variation in cluster
100 % 2 3 27443
95 % 4 5 14966 Flexibility: Low
Max RMSD: 2.8, Avg RMSD: 1.9
PDBFlex
90 % 4 5 15510
70 % 4 5 14503
50 % 4 6 10488
40 % 4 6 9474
30 % 4 6 8120
Entity #2 | Chains: P
5'-R(P*AP*GP*GP*C)-3' rna, length: 4 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
Entity #3 | 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 % 105 127 236
95 % 105 127 312 Flexibility: Low
Max RMSD: 6.8, Avg RMSD: 1.6
PDBFlex
90 % 105 127 324
70 % 107 132 347
50 % 108 145 379
40 % 108 145 407
30 % 108 145 405
Entity #4 | 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 % 105 129 233
95 % 105 129 306 Flexibility: Low
Max RMSD: 3.3, Avg RMSD: 1.2
PDBFlex
90 % 105 129 317
70 % 108 136 335
50 % 108 147 373
40 % 113 155 353
30 % 211 308 143
Entity #5 | 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 % 103 124 244
95 % 103 124 321 Flexibility: Low
Max RMSD: 1.0, Avg RMSD: 0.5
PDBFlex
90 % 103 124 332
70 % 103 124 376
50 % 103 124 444
40 % 103 124 475
30 % 103 124 480
Entity #6 | 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 % 51 66 601
95 % 51 66 738 Flexibility: Low
Max RMSD: 3.5, Avg RMSD: 0.8
PDBFlex
90 % 51 66 761
70 % 52 69 768
50 % 54 74 748
40 % 54 74 779
30 % 54 74 782
Entity #7 | 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 % 111 163 182
95 % 111 163 232 Flexibility: Low
Max RMSD: 2.1, Avg RMSD: 0.7
PDBFlex
90 % 111 163 238
70 % 113 168 254
50 % 114 170 271
40 % 114 181 278
30 % 114 181 294
Entity #8 | 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 % 108 157 186
95 % 108 157 242 Flexibility: Low
Max RMSD: 1.4, Avg RMSD: 0.6
PDBFlex
90 % 108 157 248
70 % 108 157 281
50 % 111 176 262
40 % 111 176 288
30 % 111 176 298
Entity #9 | 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 % 53 69 539
95 % 53 69 674 Flexibility: Low
Max RMSD: 4.4, Avg RMSD: 0.7
PDBFlex
90 % 53 69 699
70 % 53 69 741
50 % 57 88 561
40 % 57 88 602
30 % 57 88 605

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 5OQM 4 D DNA-directed RNA polymerase II subunit RPB4 4932
56 5OQJ 4 D DNA-directed RNA polymerase II subunit RPB4 4932
57 5VVS 4 D DNA-directed RNA polymerase II subunit RPB4 4932
58 5VVR 4 D DNA-directed RNA polymerase II subunit RPB4 4932
59 5SVA 4 D DNA-directed RNA polymerase II subunit RPB4 4932
60 5FYW 4 D DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB4 4932
61 5FZ5 4 D DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB4 4932
62 4V1N 4 D DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB4 4932
63 4V1O 4 D DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB4 4932
64 3J1N 4 D DNA-directed RNA polymerase II subunit RPB4 4932
65 3J0K 4 D DNA-directed RNA polymerase II 32 kDa polypeptide 9606 2.7.7.6 | Details
66 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