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 % 109 172 186
95 % 110 173 234 Flexibility: Low
Max RMSD: 1.9, Avg RMSD: 0.9
PDBFlex
90 % 110 173 242
70 % 110 173 269
50 % 112 185 272
40 % 112 185 307
30 % 113 201 286
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 % 104 132 240
95 % 104 132 308 Flexibility: Low
Max RMSD: 2.9, Avg RMSD: 1.0
PDBFlex
90 % 104 132 321
70 % 106 144 338
50 % 107 146 404
40 % 107 146 429
30 % 107 161 400
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 % 110 172 184
95 % 110 172 235 Flexibility: No
Max RMSD: 1.1, Avg RMSD: 0.5
PDBFlex
90 % 110 172 243
70 % 113 199 217
50 % 118 207 227
40 % 118 207 256
30 % 118 207 271
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 % 105 133 238
95 % 105 133 305 Flexibility: No
Max RMSD: 1.1, Avg RMSD: 0.5
PDBFlex
90 % 105 133 318
70 % 105 133 367
50 % 107 145 412
40 % 108 147 427
30 % 108 147 427
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 % 108 168 241 Flexibility: Low
Max RMSD: 2.0, Avg RMSD: 1.0
PDBFlex
90 % 108 168 247
70 % 108 168 282
50 % 110 180 285
40 % 110 180 319
30 % 110 180 327
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 28939
95 % 4 5 15836 Flexibility: Low
Max RMSD: 2.8, Avg RMSD: 1.9
PDBFlex
90 % 4 5 16381
70 % 4 5 15222
50 % 4 6 11002
40 % 4 6 9923
30 % 4 6 8490
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 % 105 131 247
95 % 105 131 316 Flexibility: Low
Max RMSD: 6.8, Avg RMSD: 1.6
PDBFlex
90 % 105 131 328
70 % 107 143 343
50 % 108 158 373
40 % 108 158 403
30 % 108 158 408
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 % 105 133 239
95 % 105 133 306 Flexibility: Low
Max RMSD: 3.3, Avg RMSD: 1.2
PDBFlex
90 % 105 133 319
70 % 108 147 335
50 % 108 160 365
40 % 113 168 364
30 % 219 345 142
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 % 103 128 251
95 % 103 128 325 Flexibility: Low
Max RMSD: 1.0, Avg RMSD: 0.5
PDBFlex
90 % 103 128 337
70 % 103 128 383
50 % 103 128 457
40 % 103 128 494
30 % 103 128 496
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 70 594
95 % 51 70 731 Flexibility: Low
Max RMSD: 3.5, Avg RMSD: 0.8
PDBFlex
90 % 51 70 766
70 % 52 73 771
50 % 54 85 683
40 % 54 85 715
30 % 54 85 722
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 % 111 173 183
95 % 111 173 233 Flexibility: Low
Max RMSD: 2.1, Avg RMSD: 0.7
PDBFlex
90 % 111 173 241
70 % 113 185 243
50 % 114 187 266
40 % 114 200 275
30 % 114 200 289
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 % 108 167 242 Flexibility: Low
Max RMSD: 1.4, Avg RMSD: 0.6
PDBFlex
90 % 108 167 248
70 % 108 167 284
50 % 111 195 250
40 % 111 195 283
30 % 111 195 298
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 73 554
95 % 53 73 681 Flexibility: Low
Max RMSD: 4.4, Avg RMSD: 0.7
PDBFlex
90 % 53 73 706
70 % 53 73 756
50 % 57 101 520
40 % 57 101 568
30 % 57 101 571

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 5XOG 4 D RNA polymerase II subunit B32 460519
4 4A3E 4 D DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB4 4932
5 5OT2 4 D DNA-directed RNA polymerase II subunit RPB4 4932
6 4A3D 4 D DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB4 4932
7 5IP7 4 D DNA-directed RNA polymerase II subunit RPB4 4932
8 4A3F 4 D DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB4 4932
9 4A93 4 D DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB4 4932
10 4BY7 4 D DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB4 4932
11 4A3C 4 D DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB4 4932
12 4A3K 4 D DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB4 4932
13 4A3L 4 D DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB4 4932
14 4BXX 4 D DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB4 4932
15 4A3G 4 D DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB4 4932
16 4A3B 4 D DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB4 4932
17 4BBR 4 D DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB4 4932
18 4A3J 4 D DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB4 4932
19 4A3I 4 D DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB4 4932
20 4BY1 4 D DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB4 4932
21 4A3M 4 D DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB4 4932
22 5IP9 4 D DNA-directed RNA polymerase II subunit RPB4 4932
23 4BBS 4 D DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB4 4932
24 3HOU 4 D, P DNA-directed RNA polymerase II subunit RPB4 4932 2.7.7.6 | Details
25 3HOY 4 D DNA-directed RNA polymerase II subunit RPB4 4932 2.7.7.6 | Details
26 3HOV 4 D DNA-directed RNA polymerase II subunit RPB4 4932 2.7.7.6 | Details
27 5C3E 4 D DNA-directed RNA polymerase II subunit RPB4 4932
28 3HOZ 4 D DNA-directed RNA polymerase II subunit RPB4 4932 2.7.7.6 | Details
29 3HOW 4 D DNA-directed RNA polymerase II subunit RPB4 4932 2.7.7.6 | Details
30 3HOX 4 D DNA-directed RNA polymerase II subunit RPB4 4932 2.7.7.6 | Details
31 2R92 6 D DNA-directed RNA polymerase II subunit RPB4 4932 2.7.7.6 | Details
32 2R7Z 7 D DNA-directed RNA polymerase II subunit RPB4 4932 2.7.7.6 | Details
33 3I4M 4 D DNA-directed RNA polymerase II subunit RPB4 4932
34 3H3V 4 E DNA-directed RNA polymerase II subunit RPB4 4932 2.7.7.6 | Details
35 5U5Q 4 D DNA-directed RNA polymerase II subunit RPB4 4932
36 5C4X 4 D DNA-directed RNA polymerase II subunit RPB4 4932
37 2VUM 4 D DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB4 4932 2.7.7.6 | Details
38 5C44 4 D DNA-directed RNA polymerase II subunit RPB4 4932
39 2R93 5 D DNA-directed RNA polymerase II subunit RPB4 4932 2.7.7.6 | Details
40 3I4N 4 D DNA-directed RNA polymerase II subunit RPB4 4932
41 4BXZ 4 D DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB4 4932 2.7.7.6 | Details
42 5C4A 4 D DNA-directed RNA polymerase II subunit RPB4 4932
43 3K1F 4 D DNA-directed RNA polymerase II subunit RPB4 4932 2.7.7.6 | Details
44 1WCM 4 D DNA-DIRECTED RNA POLYMERASE II 32 KDA POLYPEPTIDE NUMBERING OF RESIUDES D10-D24 IS ARBITRARY 4932 2.7.7.6 | Details
45 2JA7 7 D, P DNA-DIRECTED RNA POLYMERASE II 32KDA POLYPEPTIDE 4932 2.7.7.6 | Details
46 1Y1W 7 D DNA-directed RNA polymerase II 32 kDa polypeptide 4932 2.7.7.6 | Details
47 3QT1 4 D DNA-directed RNA polymerase II subunit RPB4 4932 2.7.7.6 | Details
48 5X50 4 D RNA polymerase II subunit B32 460519
49 2JA8 4 D DNA-DIRECTED RNA POLYMERASE II 32KDA POLYPEPTIDE 4932 2.7.7.6 | Details
50 2JA5 4 D DNA-directed RNA polymerase II subunit RPB4 4932
51 2B63 5 D DNA-directed RNA polymerase II 32 kDa polypeptide 4932 2.7.7.6 | Details
52 1Y1V 4 D DNA-directed RNA polymerase II 32 kDa polypeptide 4932 2.7.7.6 | Details
53 3FKI 4 D DNA-directed RNA polymerase II subunit RPB4 4932
54 1Y1Y 6 D DNA-directed RNA polymerase II 32 kDa polypeptide 4932 2.7.7.6 | Details
55 2JA6 4 D DNA-DIRECTED RNA POLYMERASE II 32KDA POLYPEPTIDE 4932 2.7.7.6 | Details
56 1Y77 7 D DNA-directed RNA polymerase II 32 kDa polypeptide 4932 2.7.7.6 | Details
57 2B8K 4 D DNA-directed RNA polymerase II 32 kDa polypeptide 4932 2.7.7.6 | Details
58 5X51 4 D, P RNA polymerase II subunit B32 460519
59 5X4Z 4 D, P RNA polymerase II subunit B32 460519
60 6I84 10 D DNA-directed RNA polymerase II subunit RPB4 4932
61 6GYK 4 D DNA-directed RNA polymerase II subunit RPB4 4932
62 6GYL 4 D DNA-directed RNA polymerase II subunit RPB4 4932
63 6GYM 12 D DNA-directed RNA polymerase II subunit RPB4 4932
64 6A5O 4 D RNA polymerase II subunit B32 460519
65 6A5P 4 D RNA polymerase II subunit B32 460519
66 6A5R 4 D RNA polymerase II subunit B32 460519
67 6A5T 4 D RNA polymerase II subunit B32 460519
68 6A5U 4 D RNA polymerase II subunit B32 460519
69 6A5V 4 D RNA polymerase II subunit B32 460519
70 6A5L 4 D RNA polymerase II subunit B32 460519
71 5OQM 4 D DNA-directed RNA polymerase II subunit RPB4 4932
72 5OQJ 4 D DNA-directed RNA polymerase II subunit RPB4 4932
73 5XON 4 D RNA polymerase II subunit B32 460519
74 5VVS 4 D DNA-directed RNA polymerase II subunit RPB4 4932
75 5VVR 4 D DNA-directed RNA polymerase II subunit RPB4 4932
76 5SVA 4 D DNA-directed RNA polymerase II subunit RPB4 4932
77 5FYW 4 D DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB4 4932
78 5FZ5 4 D DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB4 4932
79 5FMF 6 D RNA POLYMERASE II PRE-INITIATION COMPLEX, RPB4 4932
80 4V1N 4 D DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB4 4932
81 4V1O 4 D DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB4 4932
82 3J1N 4 D DNA-directed RNA polymerase II subunit RPB4 4932
83 3J0K 4 D DNA-directed RNA polymerase II 32 kDa polypeptide 9606 2.7.7.6 | Details
84 1PQV 4 D DNA-directed RNA polymerase II 32 kDa polypeptide 4932 2.7.7.6 | Details
85 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