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 % 110 173 270
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 % 104 132 242
95 % 104 132 309 Flexibility: Low
Max RMSD: 2.9, Avg RMSD: 1.0
PDBFlex
90 % 104 132 321
70 % 106 144 340
50 % 107 146 406
40 % 107 146 431
30 % 107 161 401
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 % 113 199 218
50 % 118 207 227
40 % 118 207 257
30 % 118 207 272
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 % 105 133 240
95 % 105 133 306 Flexibility: No
Max RMSD: 1.1, Avg RMSD: 0.5
PDBFlex
90 % 105 133 318
70 % 105 133 367
50 % 107 145 414
40 % 108 147 429
30 % 108 147 429
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 % 108 168 283
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 29076
95 % 4 5 15900 Flexibility: Low
Max RMSD: 2.8, Avg RMSD: 1.9
PDBFlex
90 % 4 5 16450
70 % 4 5 15286
50 % 4 6 11049
40 % 4 6 9957
30 % 4 6 8517
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 % 105 131 248
95 % 105 131 317 Flexibility: Low
Max RMSD: 6.8, Avg RMSD: 1.6
PDBFlex
90 % 105 131 328
70 % 107 143 345
50 % 108 158 373
40 % 108 158 404
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 % 105 133 241
95 % 105 133 307 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 % 219 347 142
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 % 103 128 252
95 % 103 128 326 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 % 103 128 497
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 70 597
95 % 51 70 735 Flexibility: Low
Max RMSD: 3.5, Avg RMSD: 0.8
PDBFlex
90 % 51 70 769
70 % 52 73 774
50 % 54 85 687
40 % 54 85 720
30 % 54 85 729
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 % 108 167 285
50 % 111 195 251
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 73 558
95 % 53 73 687 Flexibility: Low
Max RMSD: 4.4, Avg RMSD: 0.7
PDBFlex
90 % 53 73 709
70 % 53 73 759
50 % 57 101 521
40 % 57 101 568
30 % 57 101 572

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


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Rank PDB ID Entity ID Chains Description Details Taxonomy EC Number
1 1TWF 9 K DNA-directed RNA polymerase II 13.6 kDa polypeptide 4932 2.7.7.6 | Details
2 3S14 9 K DNA-directed RNA polymerase II subunit RPB11 4932
3 3CQZ 9 K DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB11 4932
4 3PO2 11 K DNA-directed RNA polymerase II subunit RPB11 4932 2.7.7.6 | Details
5 3RZO 9 K DNA-directed RNA polymerase II subunit RPB11 4932
6 3PO3 11 K DNA-directed RNA polymerase II subunit RPB11 4932 2.7.7.6 | Details
7 3S1M 9 K DNA-directed RNA polymerase II subunit RPB11 4932
8 4A3E 11 K DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB11 4932
9 5OT2 11 K DNA-directed RNA polymerase II subunit RPB11 4932
10 3S1R 9 K DNA-directed RNA polymerase II subunit RPB11 4932
11 4A3D 11 K DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB11 4932
12 3S1N 9 K DNA-directed RNA polymerase II subunit RPB11 4932
13 5IP7 11 K DNA-directed RNA polymerase II subunit RPB11 4932
14 4A3F 11 K DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB11 4932
15 4A93 11 K DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB11 4932
16 1K83 9 K DNA-DIRECTED RNA POLYMERASE II 13.6KD POLYPEPTIDE 4932 2.7.7.6 | Details
17 1I50 9 K DNA-DIRECTED RNA POLYMERASE II 13.6KD POLYPEPTIDE 4932 2.7.7.6 | Details
18 4BY7 11 K DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB11 4932
19 3S2D 9 K DNA-directed RNA polymerase II subunit RPB11 4932
20 4A3C 11 K DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB11 4932
21 4A3K 11 K DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB11 4932
22 3S15 9 K DNA-directed RNA polymerase II subunit RPB11 4932
23 4A3L 11 K DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB11 4932
24 4BXX 11 K DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB11 4932
25 3S1Q 9 K DNA-directed RNA polymerase II subunit RPB11 4932
26 3S16 9 K DNA-directed RNA polymerase II subunit RPB11 4932
27 3S17 9 K DNA-directed RNA polymerase II subunit RPB11 4932
28 4A3G 11 K DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB11 4932
29 4A3B 11 K DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB11 4932
30 4BBR 11 K DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB11 4932
31 2NVQ 12 K DNA-directed RNA polymerase II 13.6 kDa polypeptide 4932 2.7.7.6 | Details
32 3RZD 9 K DNA-directed RNA polymerase II subunit RPB11 4932
33 4A3J 11 K DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB11 4932
34 3S2H 9 K DNA-directed RNA polymerase II subunit RPB11 4932
35 3M3Y 9 K DNA-directed RNA polymerase II subunit RPB11 4932
36 4A3I 11 K DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB11 4932
37 6BM4 9 K DNA-directed RNA polymerase II subunit RPB11 4932
38 4BY1 11 K DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB11 4932
39 4A3M 11 K DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB11 4932
40 6BLP 9 K DNA-directed RNA polymerase II subunit RPB11 4932
41 4Y7N 9 K DNA-directed RNA polymerase II subunit RPB11 4932
42 5IP9 11 K DNA-directed RNA polymerase II subunit RPB11 4932
43 1I3Q 9 K DNA-DIRECTED RNA POLYMERASE II 13.6KD POLYPEPTIDE 4932 2.7.7.6 | Details
44 4BBS 11 K DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB11 4932
45 6BLO 9 K DNA-directed RNA polymerase II subunit RPB11 4932
46 1TWC 9 K DNA-directed RNA polymerase II 13.6 kDa polypeptide 4932 2.7.7.6 | Details
47 4Y52 9 K DNA-directed RNA polymerase II subunit RPB11 4932
48 6BQF 9 K DNA-directed RNA polymerase II subunit RPB11 4932
49 3HOU 11 K, W DNA-directed RNA polymerase II subunit RPB11 4932 2.7.7.6 | Details
50 3HOY 11 K DNA-directed RNA polymerase II subunit RPB11 4932 2.7.7.6 | Details
51 3HOV 11 K DNA-directed RNA polymerase II subunit RPB11 4932 2.7.7.6 | Details
52 6BM2 9 K DNA-directed RNA polymerase II subunit RPB11 4932
53 1TWA 9 K DNA-directed RNA polymerase II 13.6 kDa polypeptide 4932 2.7.7.6 | Details
54 5C3E 11 K DNA-directed RNA polymerase II subunit RPB11 4932
55 5W51 9 K DNA-directed RNA polymerase II subunit RPB11 4932
56 2NVT 12 K DNA-directed RNA polymerase II 13.6 kDa polypeptide 4932 2.7.7.6 | Details
57 3HOZ 11 K DNA-directed RNA polymerase II subunit RPB11 4932 2.7.7.6 | Details
58 3HOW 11 K DNA-directed RNA polymerase II subunit RPB11 4932 2.7.7.6 | Details
59 3HOX 11 K DNA-directed RNA polymerase II subunit RPB11 4932 2.7.7.6 | Details
60 1I6H 11 K DNA-DIRECTED RNA POLYMERASE II 13.6KD POLYPEPTIDE 4932 2.7.7.6 | Details
61 2R92 13 K DNA-directed RNA polymerase II subunit RPB11 4932 2.7.7.6 | Details
62 5W4U 9 K DNA-directed RNA polymerase II subunit RPB11 4932
63 2R7Z 14 K DNA-directed RNA polymerase II subunit RPB11 4932 2.7.7.6 | Details
64 1R9T 12 K DNA-directed RNA polymerase II 13.6 kDa polypeptide 4932 2.7.7.6 | Details
65 3I4M 11 K DNA-directed RNA polymerase II subunit RPB11 4932
66 3H3V 11 L DNA-directed RNA polymerase II subunit RPB11 4932 2.7.7.6 | Details
67 5U5Q 11 K DNA-directed RNA polymerase II subunit RPB11 4932
68 1TWH 9 K DNA-directed RNA polymerase II 13.6 kDa polypeptide 4932 2.7.7.6 | Details
69 2NVY 9 K DNA-directed RNA polymerase II 13.6 kDa polypeptide 4932 2.7.7.6 | Details
70 2E2J 12 K DNA-directed RNA polymerase II 13.6 kDa polypeptide 4932 2.7.7.6 | Details
71 5C4X 11 K DNA-directed RNA polymerase II subunit RPB11 4932
72 2VUM 11 K DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB11 4932 2.7.7.6 | Details
73 5C44 11 K DNA-directed RNA polymerase II subunit RPB11 4932
74 3M4O 9 K DNA-directed RNA polymerase II subunit RPB11 4932
75 5C4J 9 K DNA-directed RNA polymerase II subunit RPB11 4932
76 2R93 12 K DNA-directed RNA polymerase II subunit RPB11 4932 2.7.7.6 | Details
77 1TWG 9 K DNA-directed RNA polymerase II 13.6 kDa polypeptide 4932 2.7.7.6 | Details
78 3GTM 9 K DNA-directed RNA polymerase II subunit RPB11 DNA-directed RNA polymerase II 13.6 kDa polypeptide 4932
79 3I4N 11 K DNA-directed RNA polymerase II subunit RPB11 4932
80 2E2I 12 K DNA-directed RNA polymerase II 13.6 kDa polypeptide 4932 2.7.7.6 | Details
81 3GTL 9 K DNA-directed RNA polymerase II subunit RPB11 DNA-directed RNA polymerase II 13.6 kDa polypeptide 4932
82 4BXZ 11 K DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB11 4932 2.7.7.6 | Details
83 3GTK 9 K DNA-directed RNA polymerase II subunit RPB11 DNA-directed RNA polymerase II 13.6 kDa polypeptide 4932
84 5C4A 11 K DNA-directed RNA polymerase II subunit RPB11 4932
85 3K1F 11 K DNA-directed RNA polymerase II subunit RPB11 4932 2.7.7.6 | Details
86 3GTJ 9 K DNA-directed RNA polymerase II subunit RPB11 DNA-directed RNA polymerase II 13.6 kDa polypeptide 4932
87 3GTG 9 K DNA-directed RNA polymerase II subunit RPB11 DNA-directed RNA polymerase II 13.6 kDa polypeptide 4932
88 2YU9 12 K DNA-directed RNA polymerase II 13.6 kDa polypeptide 4932 2.7.7.6 | Details
89 1WCM 11 K DNA-DIRECTED RNA POLYMERASE II 13.6 KDA POLYPEPTIDE 4932 2.7.7.6 | Details
90 2JA7 14 K, W DNA-DIRECTED RNA POLYMERASE II 13.6 KDA POLYPEPTIDE 4932 2.7.7.6 | Details
91 4X6A 9 K DNA-directed RNA polymerase II subunit RPB11 4932
92 4X67 9 K DNA-directed RNA polymerase II subunit RPB11 4932
93 1Y1W 14 K DNA-directed RNA polymerase II 13.6 kDa polypeptide 4932 2.7.7.6 | Details
94 3QT1 11 K DNA-directed RNA polymerase II subunit RPB11 4932 2.7.7.6 | Details
95 3K7A 9 K DNA-directed RNA polymerase II subunit RPB11 4932
96 2JA8 11 K DNA-DIRECTED RNA POLYMERASE II 13.6 KDA POLYPEPTIDE 4932 2.7.7.6 | Details
97 2JA5 11 K DNA-directed RNA polymerase II subunit RPB11 4932
98 2NVX 12 K DNA-directed RNA polymerase II 13.6 kDa polypeptide 4932 2.7.7.6 | Details
99 2B63 12 K DNA-directed RNA polymerase II 13.6 kDa polypeptide 4932 2.7.7.6 | Details
100 3GTQ 9 K DNA-directed RNA polymerase II subunit RPB11 DNA-directed RNA polymerase II 13.6 kDa polypeptide 4932
101 3GTP 9 K DNA-directed RNA polymerase II subunit RPB11 DNA-directed RNA polymerase II 13.6 kDa polypeptide 4932
102 1Y1V 11 K DNA-directed RNA polymerase II 13.6 kDa polypeptide 4932 2.7.7.6 | Details
103 3GTO 9 K DNA-directed RNA polymerase II subunit RPB11 DNA-directed RNA polymerase II 13.6 kDa polypeptide 4932
104 3FKI 11 K DNA-directed RNA polymerase II subunit RPB11 4932
105 1Y1Y 13 K DNA-directed RNA polymerase II 13.6 kDa polypeptide 4932 2.7.7.6 | Details
106 1SFO 11 K DNA-directed RNA polymerase II 13.6 kDa polypeptide 4932 2.7.7.6 | Details
107 2E2H 12 K DNA-directed RNA polymerase II 13.6 kDa polypeptide 4932 2.7.7.6 | Details
108 2JA6 11 K DNA-DIRECTED RNA POLYMERASE II 13.6 KDA POLYPEPTIDE 4932 2.7.7.6 | Details
109 2NVZ 12 K DNA-directed RNA polymerase II 13.6 kDa polypeptide 4932 2.7.7.6 | Details
110 1Y77 14 K DNA-directed RNA polymerase II 13.6 kDa polypeptide 4932 2.7.7.6 | Details
111 1NIK 11 K DNA-directed RNA polymerase II, chain RPB11 4932 2.7.7.6 | Details
112 1R9S 11 K DNA-directed RNA polymerase II 13.6 kDa polypeptide 4932 2.7.7.6 | Details
113 1R5U 9 K DNA-directed RNA polymerase II 13.6 kDa polypeptide 4932 2.7.7.6 | Details
114 2B8K 11 K DNA-directed RNA polymerase II 13.6 kDa polypeptide 4932 2.7.7.6 | Details
115 6I84 17 K DNA-directed RNA polymerase II subunit RPB11 4932
116 6GYK 11 K DNA-directed RNA polymerase II subunit RPB11 4932
117 6GYL 11 K DNA-directed RNA polymerase II subunit RPB11 4932
118 6GYM 19 K DNA-directed RNA polymerase II subunit RPB11 4932
119 5OQM 11 K DNA-directed RNA polymerase II subunit RPB11 4932
120 5OQJ 11 K DNA-directed RNA polymerase II subunit RPB11 4932
121 5VVS 11 K DNA-directed RNA polymerase II subunit RPB11 4932
122 5VVR 11 K DNA-directed RNA polymerase II subunit RPB11 4932
123 5SVA 11 K DNA-directed RNA polymerase II subunit RPB11 4932
124 5FYW 11 K DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB11 4932
125 5FZ5 11 K DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB11 4932
126 5FMF 13 K DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB11 4932
127 4V1M 9 K DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB11 4932
128 4V1N 11 K DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB11 2.7.7.6 4932
129 4V1O 11 K DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB11 2.7.7.6 4932
130 3J1N 11 K DNA-directed RNA polymerase II subunit RPB11 4932
131 3J0K 11 K DNA-directed RNA polymerase II 13.6 kDa polypeptide 9606 2.7.7.6 | Details
132 1PQV 11 K DNA-directed RNA polymerase II 13.6 kDa polypeptide 4932 2.7.7.6 | Details
133 1NT9 11 K DNA-DIRECTED RNA POLYMERASE II 13.6 KD POLYPEPTIDE 4932 2.7.7.6 | Details