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 % 109 171 185
95 % 110 172 231 Flexibility: Low
Max RMSD: 1.9, Avg RMSD: 0.9
PDBFlex
90 % 110 172 240
70 % 110 172 268
50 % 112 184 266
40 % 112 184 302
30 % 113 200 282
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 % 104 131 240
95 % 104 131 304 Flexibility: Low
Max RMSD: 2.9, Avg RMSD: 1.0
PDBFlex
90 % 104 131 316
70 % 106 143 336
50 % 107 145 398
40 % 107 145 423
30 % 107 160 393
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 % 110 171 184
95 % 110 171 233 Flexibility: No
Max RMSD: 1.1, Avg RMSD: 0.5
PDBFlex
90 % 110 171 242
70 % 113 198 216
50 % 118 206 223
40 % 118 206 252
30 % 118 206 267
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 % 105 132 234
95 % 105 132 301 Flexibility: No
Max RMSD: 1.1, Avg RMSD: 0.5
PDBFlex
90 % 105 132 312
70 % 105 132 362
50 % 107 144 403
40 % 108 146 422
30 % 108 146 420
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 % 108 167 187
95 % 108 167 238 Flexibility: Low
Max RMSD: 2.0, Avg RMSD: 1.0
PDBFlex
90 % 108 167 245
70 % 108 167 280
50 % 110 179 278
40 % 110 179 313
30 % 110 179 321
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 28689
95 % 4 5 15692 Flexibility: Low
Max RMSD: 2.8, Avg RMSD: 1.9
PDBFlex
90 % 4 5 16250
70 % 4 5 15106
50 % 4 6 10927
40 % 4 6 9853
30 % 4 6 8435
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 % 105 130 245
95 % 105 130 313 Flexibility: Low
Max RMSD: 6.8, Avg RMSD: 1.6
PDBFlex
90 % 105 130 326
70 % 107 142 339
50 % 108 157 366
40 % 108 157 399
30 % 108 157 403
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 % 105 132 237
95 % 105 132 302 Flexibility: Low
Max RMSD: 3.3, Avg RMSD: 1.2
PDBFlex
90 % 105 132 313
70 % 108 146 332
50 % 108 159 359
40 % 113 167 357
30 % 216 340 143
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 % 103 127 248
95 % 103 127 323 Flexibility: Low
Max RMSD: 1.0, Avg RMSD: 0.5
PDBFlex
90 % 103 127 336
70 % 103 127 385
50 % 103 127 453
40 % 103 127 491
30 % 103 127 496
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 69 598
95 % 51 69 736 Flexibility: Low
Max RMSD: 3.5, Avg RMSD: 0.8
PDBFlex
90 % 51 69 769
70 % 52 72 781
50 % 54 84 680
40 % 54 84 718
30 % 54 84 722
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 % 111 172 181
95 % 111 172 230 Flexibility: Low
Max RMSD: 2.1, Avg RMSD: 0.7
PDBFlex
90 % 111 172 239
70 % 113 184 241
50 % 114 186 263
40 % 114 199 270
30 % 114 199 284
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 % 108 166 188
95 % 108 166 240 Flexibility: Low
Max RMSD: 1.4, Avg RMSD: 0.6
PDBFlex
90 % 108 166 247
70 % 108 166 283
50 % 111 194 245
40 % 111 194 277
30 % 111 194 291
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 72 551
95 % 53 72 686 Flexibility: Low
Max RMSD: 4.4, Avg RMSD: 0.7
PDBFlex
90 % 53 72 708
70 % 53 72 754
50 % 57 100 519
40 % 57 100 563
30 % 57 100 573

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 1Y14 2 B, D DNA-directed RNA polymerase II 19 kDa polypeptide 4932 2.7.7.6 | Details
2 3PO2 7 G DNA-directed RNA polymerase II subunit RPB7 4932 2.7.7.6 | Details
3 3PO3 7 G DNA-directed RNA polymerase II subunit RPB7 4932 2.7.7.6 | Details
4 4A3E 7 G RPB7, DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB7 4932
5 5OT2 7 G DNA-directed RNA polymerase II subunit RPB7 4932
6 4A3D 7 G RPB7, DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB7 4932
7 5IP7 7 G DNA-directed RNA polymerase II subunit RPB7 4932
8 4A3F 7 G RPB7, DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB7 4932
9 4A93 7 G RPB7, DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB7 4932
10 4BY7 7 G DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB7 4932
11 4A3C 7 G RPB7, DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB7 4932
12 4A3K 7 G RPB7, DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB7 4932
13 4A3L 7 G DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB7 4932
14 4BXX 7 G DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB7 4932
15 4A3G 7 G RPB7, DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB7 4932
16 4A3B 7 G RPB7, DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB7 4932
17 4BBR 7 G DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB7 4932
18 4A3J 7 G RPB7, DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB7 4932
19 4A3I 7 G RPB7, DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB7 4932
20 4BY1 7 G DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB7 4932
21 4A3M 7 G DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB7 4932
22 5IP9 7 G DNA-directed RNA polymerase II subunit RPB7 4932
23 4BBS 7 G DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB7 4932
24 3HOU 7 G, S DNA-directed RNA polymerase II subunit RPB7 4932 2.7.7.6 | Details
25 3HOY 7 G DNA-directed RNA polymerase II subunit RPB7 4932 2.7.7.6 | Details
26 3HOV 7 G DNA-directed RNA polymerase II subunit RPB7 4932 2.7.7.6 | Details
27 5C3E 7 G DNA-directed RNA polymerase II subunit RPB7 4932
28 3HOZ 7 G DNA-directed RNA polymerase II subunit RPB7 4932 2.7.7.6 | Details
29 3HOW 7 G DNA-directed RNA polymerase II subunit RPB7 4932 2.7.7.6 | Details
30 3HOX 7 G DNA-directed RNA polymerase II subunit RPB7 4932 2.7.7.6 | Details
31 2R92 9 G DNA-directed RNA polymerase II subunit RPB7 4932 2.7.7.6 | Details
32 2R7Z 10 G DNA-directed RNA polymerase II subunit RPB7 4932 2.7.7.6 | Details
33 3I4M 7 G DNA-directed RNA polymerase II subunit RPB7 4932
34 3H3V 7 H DNA-directed RNA polymerase II subunit RPB7 4932 2.7.7.6 | Details
35 5U5Q 7 G DNA-directed RNA polymerase II subunit RPB7 4932
36 5C4X 7 G DNA-directed RNA polymerase II subunit RPB7 4932
37 2VUM 7 G DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB7 4932 2.7.7.6 | Details
38 5C44 7 G DNA-directed RNA polymerase II subunit RPB7 4932
39 2R93 8 G DNA-directed RNA polymerase II subunit RPB7 4932 2.7.7.6 | Details
40 3I4N 7 G DNA-directed RNA polymerase II subunit RPB7 4932
41 4BXZ 7 G DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB7 4932 2.7.7.6 | Details
42 5C4A 7 G DNA-directed RNA polymerase II subunit RPB7 4932
43 3K1F 7 G DNA-directed RNA polymerase II subunit RPB7 4932 2.7.7.6 | Details
44 1WCM 7 G DNA-DIRECTED RNA POLYMERASE II 19 KD POLYPEPTIDE 4932 2.7.7.6 | Details
45 2JA7 10 G, S DNA-DIRECTED RNA POLYMERASE II 19KDA POLYPEPTIDE 4932 2.7.7.6 | Details
46 1Y1W 10 G DNA-directed RNA polymerase II 19 kDa polypeptide 4932 2.7.7.6 | Details
47 3QT1 7 G DNA-directed RNA polymerase II subunit RPB7 4932 2.7.7.6 | Details
48 2JA8 7 G DNA-DIRECTED RNA POLYMERASE II 19KDA POLYPEPTIDE 4932 2.7.7.6 | Details
49 2JA5 7 G DNA-directed RNA polymerase II subunit RPB7 4932
50 2B63 8 G DNA-directed RNA polymerase II 19 kDa polypeptide 4932 2.7.7.6 | Details
51 1Y1V 7 G DNA-directed RNA polymerase II 19 kDa polypeptide 4932 2.7.7.6 | Details
52 3FKI 7 G DNA-directed RNA polymerase II subunit RPB7 4932
53 1Y1Y 9 G DNA-directed RNA polymerase II 19 kDa polypeptide 4932 2.7.7.6 | Details
54 2JA6 7 G DNA-DIRECTED RNA POLYMERASE II 19KDA POLYPEPTIDE 4932 2.7.7.6 | Details
55 1Y77 10 G DNA-directed RNA polymerase II 19 kDa polypeptide 4932 2.7.7.6 | Details
56 6GYK 7 G DNA-directed RNA polymerase II subunit RPB7 4932
57 6GYL 7 G DNA-directed RNA polymerase II subunit RPB7 4932
58 6GYM 15 G DNA-directed RNA polymerase II subunit RPB7 4932
59 5OQM 7 G DNA-directed RNA polymerase II subunit RPB7 4932
60 5OQJ 7 G DNA-directed RNA polymerase II subunit RPB7 4932
61 5VVS 7 G DNA-directed RNA polymerase II subunit RPB7 4932
62 5VVR 7 G DNA-directed RNA polymerase II subunit RPB7 4932
63 5SVA 7 G DNA-directed RNA polymerase II subunit RPB7 4932
64 5FYW 7 G DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB7 4932
65 5FZ5 7 G DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB7 4932
66 5FMF 9 G DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB7 4932
67 4V1N 7 G DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB7 4932
68 4V1O 7 G DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB7 4932
69 3J1N 7 G DNA-directed RNA polymerase II subunit RPB7 4932
70 3J0K 7 G DNA-directed RNA polymerase II 19 kDa polypeptide 9606 2.7.7.6 | Details
71 1PQV 7 G DNA-directed RNA polymerase II 19 kDa polypeptide 4932 2.7.7.6 | Details
72 1NT9 7 G DNA-DIRECTED RNA POLYMERASE II 19 KD POLYPEPTIDE 4932 2.7.7.6 | Details