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 1TWF 3 C DNA-directed RNA polymerase II 45 kDa polypeptide 4932 2.7.7.6 | Details
2 3S14 3 C DNA-directed RNA polymerase II subunit RPB3 4932
3 3CQZ 3 C DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB3 4932
4 3PO2 3 C DNA-directed RNA polymerase II subunit RPB3 4932 2.7.7.6 | Details
5 3RZO 3 C DNA-directed RNA polymerase II subunit RPB3 4932
6 3PO3 3 C DNA-directed RNA polymerase II subunit RPB3 4932 2.7.7.6 | Details
7 3S1M 3 C DNA-directed RNA polymerase II subunit RPB3 4932
8 4A3E 3 C DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB3 4932
9 5OT2 3 C DNA-directed RNA polymerase II subunit RPB3 4932
10 3S1R 3 C DNA-directed RNA polymerase II subunit RPB3 4932
11 4A3D 3 C DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB3 4932
12 3S1N 3 C DNA-directed RNA polymerase II subunit RPB3 4932
13 4A3F 3 C DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB3 4932
14 4A93 3 C DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB3 4932
15 1K83 3 C DNA-DIRECTED RNA POLYMERASE II 45KD POLYPEPTIDE 4932 2.7.7.6 | Details
16 1I50 3 C DNA-DIRECTED RNA POLYMERASE II 45KD POLYPEPTIDE 4932 2.7.7.6 | Details
17 4BY7 3 C DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB3 4932
18 3S2D 3 C DNA-directed RNA polymerase II subunit RPB3 4932
19 4A3C 3 C DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB3 4932
20 4A3K 3 C DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB3 4932
21 3S15 3 C DNA-directed RNA polymerase II subunit RPB3 4932
22 4A3L 3 C DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB3 4932
23 4BXX 3 C DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB3 4932
24 3S1Q 3 C DNA-directed RNA polymerase II subunit RPB3 4932
25 3S16 3 C DNA-directed RNA polymerase II subunit RPB3 4932
26 3S17 3 C DNA-directed RNA polymerase II subunit RPB3 4932
27 4A3G 3 C DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB3 4932
28 4A3B 3 C DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB3 4932
29 4BBR 3 C DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB3 4932
30 2NVQ 6 C DNA-directed RNA polymerase II 45 kDa polypeptide 4932 2.7.7.6 | Details
31 3RZD 3 C DNA-directed RNA polymerase II subunit RPB3 4932
32 4A3J 3 C DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB3 4932
33 3S2H 3 C DNA-directed RNA polymerase II subunit RPB3 4932
34 3M3Y 3 C DNA-directed RNA polymerase II subunit RPB3 4932
35 4A3I 3 C DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB3 4932
36 6BM4 3 C DNA-directed RNA polymerase II subunit RPB3 4932
37 4BY1 3 C DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB3 4932
38 4A3M 3 C DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB3 4932
39 6BLP 3 C DNA-directed RNA polymerase II subunit RPB3 4932
40 4Y7N 3 C DNA-directed RNA polymerase II subunit RPB3 4932
41 1I3Q 3 C DNA-DIRECTED RNA POLYMERASE II 45KD POLYPEPTIDE 4932 2.7.7.6 | Details
42 4BBS 3 C DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB3 4932
43 6BLO 3 C DNA-directed RNA polymerase II subunit RPB3 4932
44 1TWC 3 C DNA-directed RNA polymerase II 45 kDa polypeptide 4932 2.7.7.6 | Details
45 4Y52 3 C DNA-directed RNA polymerase II subunit RPB3 4932
46 6BQF 3 C DNA-directed RNA polymerase II subunit RPB3 4932
47 3HOU 3 C, O DNA-directed RNA polymerase II subunit RPB3 4932 2.7.7.6 | Details
48 3HOY 3 C DNA-directed RNA polymerase II subunit RPB3 4932 2.7.7.6 | Details
49 3HOV 3 C DNA-directed RNA polymerase II subunit RPB3 4932 2.7.7.6 | Details
50 6BM2 3 C DNA-directed RNA polymerase II subunit RPB3 4932
51 1TWA 3 C DNA-directed RNA polymerase II 45 kDa polypeptide 4932 2.7.7.6 | Details
52 5C3E 3 C DNA-directed RNA polymerase II subunit RPB3 4932
53 5W51 3 C DNA-directed RNA polymerase II subunit RPB3 4932
54 2NVT 6 C DNA-directed RNA polymerase II 45 kDa polypeptide 4932 2.7.7.6 | Details
55 3HOZ 3 C DNA-directed RNA polymerase II subunit RPB3 4932 2.7.7.6 | Details
56 3HOW 3 C DNA-directed RNA polymerase II subunit RPB3 4932 2.7.7.6 | Details
57 3HOX 3 C DNA-directed RNA polymerase II subunit RPB3 4932 2.7.7.6 | Details
58 1I6H 5 C DNA-DIRECTED RNA POLYMERASE II 45KD POLYPEPTIDE 4932 2.7.7.6 | Details
59 2R92 5 C DNA-directed RNA polymerase II subunit RPB3 4932 2.7.7.6 | Details
60 5W4U 3 C DNA-directed RNA polymerase II subunit RPB3 4932
61 2R7Z 6 C DNA-directed RNA polymerase II subunit RPB3 4932 2.7.7.6 | Details
62 1R9T 6 C DNA-directed RNA polymerase II 45 kDa polypeptide 4932 2.7.7.6 | Details
63 3I4M 3 C DNA-directed RNA polymerase II subunit RPB3 4932
64 3H3V 3 D DNA-directed RNA polymerase II subunit RPB3 4932 2.7.7.6 | Details
65 5U5Q 3 C DNA-directed RNA polymerase II subunit RPB3 4932
66 1TWH 3 C DNA-directed RNA polymerase II 45 kDa polypeptide 4932 2.7.7.6 | Details
67 2NVY 3 C DNA-directed RNA polymerase II 45 kDa polypeptide 4932 2.7.7.6 | Details
68 2E2J 6 C DNA-directed RNA polymerase II 45 kDa polypeptide 4932 2.7.7.6 | Details
69 5C4X 3 C DNA-directed RNA polymerase II subunit RPB3 4932
70 2VUM 3 C DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB3 4932 2.7.7.6 | Details
71 5C44 3 C DNA-directed RNA polymerase II subunit RPB3 4932
72 3M4O 3 C DNA-directed RNA polymerase II subunit RPB3 4932
73 5C4J 3 C DNA-directed RNA polymerase II subunit RPB3 4932
74 2R93 4 C DNA-directed RNA polymerase II subunit RPB3 4932 2.7.7.6 | Details
75 1TWG 3 C DNA-directed RNA polymerase II 45 kDa polypeptide 4932 2.7.7.6 | Details
76 3GTM 3 C DNA-directed RNA polymerase II subunit RPB3 DNA-directed RNA polymerase II 45 kDa polypeptide 4932
77 3I4N 3 C DNA-directed RNA polymerase II subunit RPB3 4932
78 2E2I 6 C DNA-directed RNA polymerase II 45 kDa polypeptide 4932 2.7.7.6 | Details
79 3GTL 3 C DNA-directed RNA polymerase II subunit RPB3 DNA-directed RNA polymerase II 45 kDa polypeptide 4932
80 4BXZ 3 C DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB3 4932 2.7.7.6 | Details
81 3GTK 3 C DNA-directed RNA polymerase II subunit RPB3 DNA-directed RNA polymerase II 45 kDa polypeptide 4932
82 5C4A 3 C DNA-directed RNA polymerase II subunit RPB3 4932
83 3K1F 3 C DNA-directed RNA polymerase II subunit RPB3 4932 2.7.7.6 | Details
84 3GTJ 3 C DNA-directed RNA polymerase II subunit RPB3 DNA-directed RNA polymerase II 45 kDa polypeptide 4932
85 3GTG 3 C DNA-directed RNA polymerase II subunit RPB3 DNA-directed RNA polymerase II 45 kDa polypeptide 4932
86 2YU9 6 C DNA-directed RNA polymerase II 45 kDa polypeptide 4932 2.7.7.6 | Details
87 1WCM 3 C DNA-DIRECTED RNA POLYMERASE II 45 KDA POLYPEPTIDE 4932 2.7.7.6 | Details
88 2JA7 6 C, O DNA-DIRECTED RNA POLYMERASE II 45KDA POLYPEPTIDE 4932 2.7.7.6 | Details
89 4X6A 3 C DNA-directed RNA polymerase II subunit RPB3 4932
90 4X67 3 C DNA-directed RNA polymerase II subunit RPB3 4932
91 1Y1W 6 C DNA-directed RNA polymerase II 45 kDa polypeptide 4932 2.7.7.6 | Details
92 3QT1 3 C DNA-directed RNA polymerase II subunit RPB3 4932 2.7.7.6 | Details
93 3K7A 3 C DNA-directed RNA polymerase II subunit RPB3 4932
94 2JA8 3 C DNA-DIRECTED RNA POLYMERASE II 45KDA POLYPEPTIDE 4932 2.7.7.6 | Details
95 2JA5 3 C DNA-directed RNA polymerase II subunit RPB3 4932
96 2NVX 6 C DNA-directed RNA polymerase II 45 kDa polypeptide 4932 2.7.7.6 | Details
97 2B63 4 C DNA-directed RNA polymerase II 45 kDa polypeptide 4932 2.7.7.6 | Details
98 3GTQ 3 C DNA-directed RNA polymerase II subunit RPB3 DNA-directed RNA polymerase II 45 kDa polypeptide 4932
99 3GTP 3 C DNA-directed RNA polymerase II subunit RPB3 DNA-directed RNA polymerase II 45 kDa polypeptide 4932
100 1Y1V 3 C DNA-directed RNA polymerase II 45 kDa polypeptide 4932 2.7.7.6 | Details
101 3GTO 3 C DNA-directed RNA polymerase II subunit RPB3 DNA-directed RNA polymerase II 45 kDa polypeptide 4932
102 3FKI 3 C DNA-directed RNA polymerase II subunit RPB3 4932
103 1Y1Y 5 C DNA-directed RNA polymerase II 45 kDa polypeptide 4932 2.7.7.6 | Details
104 1SFO 5 C DNA-directed RNA polymerase II 45 kDa polypeptide 4932 2.7.7.6 | Details
105 2E2H 6 C DNA-directed RNA polymerase II 45 kDa polypeptide 4932 2.7.7.6 | Details
106 2JA6 3 C DNA-DIRECTED RNA POLYMERASE II 45KDA POLYPEPTIDE 4932 2.7.7.6 | Details
107 2NVZ 6 C DNA-directed RNA polymerase II 45 kDa polypeptide 4932 2.7.7.6 | Details
108 1Y77 6 C DNA-directed RNA polymerase II 45 kDa polypeptide 4932 2.7.7.6 | Details
109 1NIK 3 C DNA-directed RNA polymerase II, chain RPB3 4932 2.7.7.6 | Details
110 1R9S 5 C DNA-directed RNA polymerase II 45 kDa polypeptide 4932 2.7.7.6 | Details
111 1R5U 3 C DNA-directed RNA polymerase II 45 kDa polypeptide 4932 2.7.7.6 | Details
112 2B8K 3 C DNA-directed RNA polymerase II 45 kDa polypeptide 4932 2.7.7.6 | Details
113 6I84 9 C DNA-directed RNA polymerase II subunit RPB3 4932
114 6GYK 3 C DNA-directed RNA polymerase II subunit RPB3 4932
115 6GYL 3 C DNA-directed RNA polymerase II subunit RPB3 4932
116 6GYM 11 C DNA-directed RNA polymerase II subunit RPB3 4932
117 5OQM 3 C DNA-directed RNA polymerase II subunit RPB3 4932
118 5OQJ 3 C DNA-directed RNA polymerase II subunit RPB3 4932
119 5VVS 3 C DNA-directed RNA polymerase II subunit RPB3 4932
120 5VVR 3 C DNA-directed RNA polymerase II subunit RPB3 4932
121 5SVA 3 C DNA-directed RNA polymerase II subunit RPB3 4932
122 5FYW 3 C DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB3 4932
123 5FZ5 3 C DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB3 4932
124 4V1M 3 C DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB3 4932
125 4V1N 3 C DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB3 4932
126 4V1O 3 C DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB3 4932
127 1PQV 3 C DNA-directed RNA polymerase II 45 kDa polypeptide 4932 2.7.7.6 | Details
128 1NT9 3 C DNA-directed RNA polymerase II 45 kDa polypeptide 4932 2.7.7.6 | Details