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 % 109 162 184
95 % 110 163 231 Flexibility: Low
Max RMSD: 1.9, Avg RMSD: 0.9
PDBFlex
90 % 110 163 240
70 % 110 163 271
50 % 112 168 282
40 % 112 168 314
30 % 113 182 288
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 % 104 128 234
95 % 104 128 307 Flexibility: Low
Max RMSD: 2.9, Avg RMSD: 1.0
PDBFlex
90 % 104 128 318
70 % 106 133 343
50 % 107 135 404
40 % 107 135 428
30 % 107 146 404
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 % 110 162 183
95 % 110 162 233 Flexibility: No
Max RMSD: 1.1, Avg RMSD: 0.5
PDBFlex
90 % 110 162 241
70 % 113 180 230
50 % 118 188 229
40 % 118 188 254
30 % 118 188 274
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 % 105 129 232
95 % 105 129 300 Flexibility: No
Max RMSD: 1.1, Avg RMSD: 0.5
PDBFlex
90 % 105 129 312
70 % 105 129 361
50 % 107 134 407
40 % 108 136 425
30 % 108 136 426
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 % 108 158 185
95 % 108 158 241 Flexibility: Low
Max RMSD: 2.0, Avg RMSD: 1.0
PDBFlex
90 % 108 158 247
70 % 108 158 278
50 % 110 163 296
40 % 110 163 327
30 % 110 163 334
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 27443
95 % 4 5 14966 Flexibility: Low
Max RMSD: 2.8, Avg RMSD: 1.9
PDBFlex
90 % 4 5 15510
70 % 4 5 14503
50 % 4 6 10488
40 % 4 6 9474
30 % 4 6 8120
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 % 105 127 236
95 % 105 127 312 Flexibility: Low
Max RMSD: 6.8, Avg RMSD: 1.6
PDBFlex
90 % 105 127 324
70 % 107 132 347
50 % 108 145 379
40 % 108 145 407
30 % 108 145 405
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 % 105 129 233
95 % 105 129 306 Flexibility: Low
Max RMSD: 3.3, Avg RMSD: 1.2
PDBFlex
90 % 105 129 317
70 % 108 136 335
50 % 108 147 373
40 % 113 155 353
30 % 211 308 143
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 % 103 124 244
95 % 103 124 321 Flexibility: Low
Max RMSD: 1.0, Avg RMSD: 0.5
PDBFlex
90 % 103 124 332
70 % 103 124 376
50 % 103 124 444
40 % 103 124 475
30 % 103 124 480
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 66 601
95 % 51 66 738 Flexibility: Low
Max RMSD: 3.5, Avg RMSD: 0.8
PDBFlex
90 % 51 66 761
70 % 52 69 768
50 % 54 74 748
40 % 54 74 779
30 % 54 74 782
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 % 111 163 182
95 % 111 163 232 Flexibility: Low
Max RMSD: 2.1, Avg RMSD: 0.7
PDBFlex
90 % 111 163 238
70 % 113 168 254
50 % 114 170 271
40 % 114 181 278
30 % 114 181 294
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 % 108 157 186
95 % 108 157 242 Flexibility: Low
Max RMSD: 1.4, Avg RMSD: 0.6
PDBFlex
90 % 108 157 248
70 % 108 157 281
50 % 111 176 262
40 % 111 176 288
30 % 111 176 298
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 69 539
95 % 53 69 674 Flexibility: Low
Max RMSD: 4.4, Avg RMSD: 0.7
PDBFlex
90 % 53 69 699
70 % 53 69 741
50 % 57 88 561
40 % 57 88 602
30 % 57 88 605

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 5OQM 3 C DNA-directed RNA polymerase II subunit RPB3 4932
114 5OQJ 3 C DNA-directed RNA polymerase II subunit RPB3 4932
115 5VVS 3 C DNA-directed RNA polymerase II subunit RPB3 4932
116 5VVR 3 C DNA-directed RNA polymerase II subunit RPB3 4932
117 5SVA 3 C DNA-directed RNA polymerase II subunit RPB3 4932
118 5FYW 3 C DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB3 4932
119 5FZ5 3 C DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB3 4932
120 4V1M 3 C DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB3 4932
121 4V1N 3 C DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB3 4932
122 4V1O 3 C DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB3 4932
123 1PQV 3 C DNA-directed RNA polymerase II 45 kDa polypeptide 4932 2.7.7.6 | Details
124 1NT9 3 C DNA-directed RNA polymerase II 45 kDa polypeptide 4932 2.7.7.6 | Details