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 % 109 172 187
95 % 110 173 236 Flexibility: Low
Max RMSD: 1.9, Avg RMSD: 1.0
PDBFlex
90 % 110 173 243
70 % 110 173 276
50 % 112 192 266
40 % 112 192 296
30 % 113 208 281
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 % 104 132 248
95 % 104 132 315 Flexibility: Low
Max RMSD: 2.9, Avg RMSD: 1.0
PDBFlex
90 % 104 132 324
70 % 106 151 332
50 % 107 153 392
40 % 107 153 418
30 % 107 168 392
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 % 110 172 185
95 % 110 172 238 Flexibility: No
Max RMSD: 1.1, Avg RMSD: 0.5
PDBFlex
90 % 110 172 245
70 % 113 206 207
50 % 118 214 224
40 % 118 214 253
30 % 118 214 266
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 % 105 133 245
95 % 105 133 312 Flexibility: No
Max RMSD: 1.1, Avg RMSD: 0.5
PDBFlex
90 % 105 133 321
70 % 105 133 370
50 % 107 152 402
40 % 108 154 417
30 % 108 154 419
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 % 108 168 190
95 % 108 168 244 Flexibility: Low
Max RMSD: 2.0, Avg RMSD: 1.0
PDBFlex
90 % 108 168 249
70 % 108 168 288
50 % 110 187 273
40 % 110 187 308
30 % 110 187 317
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 29354
95 % 4 5 16015 Flexibility: Low
Max RMSD: 2.8, Avg RMSD: 1.9
PDBFlex
90 % 4 5 16587
70 % 4 5 15409
50 % 4 6 11166
40 % 4 6 10064
30 % 4 6 8617
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 % 105 131 253
95 % 105 131 322 Flexibility: Low
Max RMSD: 6.8, Avg RMSD: 1.6
PDBFlex
90 % 105 131 332
70 % 107 150 337
50 % 108 165 357
40 % 108 165 394
30 % 108 165 398
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 % 105 133 244
95 % 105 133 311 Flexibility: Low
Max RMSD: 3.3, Avg RMSD: 1.2
PDBFlex
90 % 105 133 320
70 % 108 154 323
50 % 108 167 354
40 % 113 175 347
30 % 226 361 142
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 % 103 128 256
95 % 103 128 330 Flexibility: Low
Max RMSD: 1.0, Avg RMSD: 0.5
PDBFlex
90 % 103 128 340
70 % 103 128 388
50 % 103 128 465
40 % 103 128 506
30 % 103 128 504
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 70 607
95 % 51 70 743 Flexibility: Low
Max RMSD: 3.5, Avg RMSD: 0.8
PDBFlex
90 % 51 70 777
70 % 52 73 786
50 % 54 92 638
40 % 54 92 668
30 % 54 92 671
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 % 111 173 183
95 % 111 173 234 Flexibility: Low
Max RMSD: 2.1, Avg RMSD: 0.7
PDBFlex
90 % 111 173 242
70 % 113 192 235
50 % 114 194 257
40 % 114 207 269
30 % 114 207 283
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 % 108 167 191
95 % 108 167 245 Flexibility: Low
Max RMSD: 1.4, Avg RMSD: 0.6
PDBFlex
90 % 108 167 250
70 % 108 167 292
50 % 111 202 248
40 % 111 202 277
30 % 111 202 290
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 73 568
95 % 53 73 698 Flexibility: Low
Max RMSD: 4.4, Avg RMSD: 0.7
PDBFlex
90 % 53 73 722
70 % 53 73 770
50 % 57 108 500
40 % 57 108 555
30 % 57 108 552

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 2C35 2 B, D, F, H DNA-DIRECTED RNA POLYMERASE II 19 KDA POLYPEPTIDE 9606
5 5XOG 7 G RNA polymerase II subunit 460519
6 4A3E 7 G RPB7, DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB7 4932
7 5OT2 7 G DNA-directed RNA polymerase II subunit RPB7 4932
8 4A3D 7 G RPB7, DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB7 4932
9 5IP7 7 G DNA-directed RNA polymerase II subunit RPB7 4932
10 4A3F 7 G RPB7, DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB7 4932
11 4A93 7 G RPB7, DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB7 4932
12 4BY7 7 G DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB7 4932
13 4A3C 7 G RPB7, DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB7 4932
14 4A3K 7 G RPB7, DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB7 4932
15 4A3L 7 G DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB7 4932
16 4BXX 7 G DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB7 4932
17 4A3G 7 G RPB7, DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB7 4932
18 4A3B 7 G RPB7, DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB7 4932
19 4BBR 7 G DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB7 4932
20 4A3J 7 G RPB7, DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB7 4932
21 4A3I 7 G RPB7, DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB7 4932
22 4BY1 7 G DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB7 4932
23 4A3M 7 G DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB7 4932
24 5IP9 7 G DNA-directed RNA polymerase II subunit RPB7 4932
25 4BBS 7 G DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB7 4932
26 3HOU 7 G, S DNA-directed RNA polymerase II subunit RPB7 4932 2.7.7.6 | Details
27 3HOY 7 G DNA-directed RNA polymerase II subunit RPB7 4932 2.7.7.6 | Details
28 3HOV 7 G DNA-directed RNA polymerase II subunit RPB7 4932 2.7.7.6 | Details
29 5C3E 7 G DNA-directed RNA polymerase II subunit RPB7 4932
30 3HOZ 7 G DNA-directed RNA polymerase II subunit RPB7 4932 2.7.7.6 | Details
31 3HOW 7 G DNA-directed RNA polymerase II subunit RPB7 4932 2.7.7.6 | Details
32 3HOX 7 G DNA-directed RNA polymerase II subunit RPB7 4932 2.7.7.6 | Details
33 2R92 9 G DNA-directed RNA polymerase II subunit RPB7 4932 2.7.7.6 | Details
34 2R7Z 10 G DNA-directed RNA polymerase II subunit RPB7 4932 2.7.7.6 | Details
35 3I4M 7 G DNA-directed RNA polymerase II subunit RPB7 4932
36 3H3V 7 H DNA-directed RNA polymerase II subunit RPB7 4932 2.7.7.6 | Details
37 5U5Q 7 G DNA-directed RNA polymerase II subunit RPB7 4932
38 5C4X 7 G DNA-directed RNA polymerase II subunit RPB7 4932
39 2VUM 7 G DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB7 4932 2.7.7.6 | Details
40 5C44 7 G DNA-directed RNA polymerase II subunit RPB7 4932
41 2R93 8 G DNA-directed RNA polymerase II subunit RPB7 4932 2.7.7.6 | Details
42 3I4N 7 G DNA-directed RNA polymerase II subunit RPB7 4932
43 4BXZ 7 G DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB7 4932 2.7.7.6 | Details
44 5C4A 7 G DNA-directed RNA polymerase II subunit RPB7 4932
45 3K1F 7 G DNA-directed RNA polymerase II subunit RPB7 4932 2.7.7.6 | Details
46 1WCM 7 G DNA-DIRECTED RNA POLYMERASE II 19 KD POLYPEPTIDE 4932 2.7.7.6 | Details
47 2JA7 10 G, S DNA-DIRECTED RNA POLYMERASE II 19KDA POLYPEPTIDE 4932 2.7.7.6 | Details
48 1Y1W 10 G DNA-directed RNA polymerase II 19 kDa polypeptide 4932 2.7.7.6 | Details
49 3QT1 7 G DNA-directed RNA polymerase II subunit RPB7 4932 2.7.7.6 | Details
50 5X50 7 G RNA polymerase II subunit 460519
51 2JA8 7 G DNA-DIRECTED RNA POLYMERASE II 19KDA POLYPEPTIDE 4932 2.7.7.6 | Details
52 2JA5 7 G DNA-directed RNA polymerase II subunit RPB7 4932
53 2B63 8 G DNA-directed RNA polymerase II 19 kDa polypeptide 4932 2.7.7.6 | Details
54 1Y1V 7 G DNA-directed RNA polymerase II 19 kDa polypeptide 4932 2.7.7.6 | Details
55 3H0G 7 G, S DNA-directed RNA polymerase II subunit rpb7 4896
56 3FKI 7 G DNA-directed RNA polymerase II subunit RPB7 4932
57 1Y1Y 9 G DNA-directed RNA polymerase II 19 kDa polypeptide 4932 2.7.7.6 | Details
58 2JA6 7 G DNA-DIRECTED RNA POLYMERASE II 19KDA POLYPEPTIDE 4932 2.7.7.6 | Details
59 1Y77 10 G DNA-directed RNA polymerase II 19 kDa polypeptide 4932 2.7.7.6 | Details
60 5X51 7 G, S RNA polymerase II subunit 460519
61 5X4Z 7 G, S RNA polymerase II subunit 460519
62 6J4W 7 G RNA polymerase II subunit 460519
63 6J4X 7 G RNA polymerase II subunit 460519
64 6J4Y 7 G RNA polymerase II subunit 460519
65 6J4Z 7 G RNA polymerase II subunit 460519
66 6J50 7 G RNA polymerase II subunit 460519
67 6J51 7 G RNA polymerase II subunit 460519
68 6I84 13 G DNA-directed RNA polymerase II subunit RPB7 4932
69 6IR9 7 G RNA polymerase II subunit 460519
70 6GYK 7 G DNA-directed RNA polymerase II subunit RPB7 4932
71 6GYL 7 G DNA-directed RNA polymerase II subunit RPB7 4932
72 6GYM 15 G DNA-directed RNA polymerase II subunit RPB7 4932
73 6A5O 7 G RNA polymerase II subunit 460519
74 6A5P 7 G RNA polymerase II subunit 460519
75 6A5R 7 G RNA polymerase II subunit 460519
76 6A5T 7 G RNA polymerase II subunit 460519
77 6A5U 7 G RNA polymerase II subunit 460519
78 6A5V 7 G RNA polymerase II subunit 460519
79 6A5L 7 G RNA polymerase II subunit 460519
80 6GML 21 G RNA polymerase II subunit G 9823
81 6GMH 7 G RNA polymerase II subunit G 9823
82 6EXV 7 G DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB7 9823
83 5OQM 7 G DNA-directed RNA polymerase II subunit RPB7 4932
84 5OQJ 7 G DNA-directed RNA polymerase II subunit RPB7 4932
85 5OIK 7 G DNA-directed RNA polymerase II subunit RPB7 9913
86 5XON 7 G RNA polymerase II subunit 460519
87 5VVS 7 G DNA-directed RNA polymerase II subunit RPB7 4932
88 5VVR 7 G DNA-directed RNA polymerase II subunit RPB7 4932
89 5U0S 23 g RNA polymerase II subunit Rpb7 4896
90 5SVA 7 G DNA-directed RNA polymerase II subunit RPB7 4932
91 5IY6 7 G DNA-directed RNA polymerase II subunit RPB7 9606
92 5IY7 7 G DNA-directed RNA polymerase II subunit RPB7 9606
93 5IY8 7 G DNA-directed RNA polymerase II subunit RPB7 9606
94 5IY9 7 G DNA-directed RNA polymerase II subunit RPB7 9606
95 5IYA 7 G DNA-directed RNA polymerase II subunit RPB7 9606
96 5IYB 7 G DNA-directed RNA polymerase II subunit RPB7 9606
97 5IYC 7 G DNA-directed RNA polymerase II subunit RPB7 9606
98 5IYD 7 G DNA-directed RNA polymerase II subunit RPB7 9606
99 5FYW 7 G DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB7 4932
100 5FZ5 7 G DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB7 4932
101 5FMF 9 G DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB7 4932
102 5FLM 7 G DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB7 9913
103 4V1N 7 G DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB7 4932
104 4V1O 7 G DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB7 4932
105 3J1N 7 G DNA-directed RNA polymerase II subunit RPB7 4932
106 3J0K 7 G DNA-directed RNA polymerase II 19 kDa polypeptide 9606 2.7.7.6 | Details
107 1PQV 7 G DNA-directed RNA polymerase II 19 kDa polypeptide 4932 2.7.7.6 | Details
108 1NT9 7 G DNA-DIRECTED RNA POLYMERASE II 19 KD POLYPEPTIDE 4932 2.7.7.6 | Details