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 % 109 168 186
95 % 110 169 234 Flexibility: Low
Max RMSD: 1.9, Avg RMSD: 0.9
PDBFlex
90 % 110 169 241
70 % 110 169 267
50 % 112 174 278
40 % 112 174 304
30 % 113 190 286
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 % 104 128 241
95 % 104 128 314 Flexibility: Low
Max RMSD: 2.9, Avg RMSD: 1.0
PDBFlex
90 % 104 128 325
70 % 106 133 351
50 % 107 135 415
40 % 107 135 440
30 % 107 150 403
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 % 110 168 185
95 % 110 168 236 Flexibility: No
Max RMSD: 1.1, Avg RMSD: 0.5
PDBFlex
90 % 110 168 243
70 % 113 188 230
50 % 118 196 231
40 % 118 196 255
30 % 118 196 269
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 % 105 129 237
95 % 105 129 306 Flexibility: No
Max RMSD: 1.1, Avg RMSD: 0.5
PDBFlex
90 % 105 129 318
70 % 105 129 370
50 % 107 134 418
40 % 108 136 435
30 % 108 136 436
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 % 108 164 187
95 % 108 164 238 Flexibility: Low
Max RMSD: 2.0, Avg RMSD: 1.0
PDBFlex
90 % 108 164 247
70 % 108 164 273
50 % 110 169 289
40 % 110 169 320
30 % 110 169 328
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 28081
95 % 4 5 15324 Flexibility: Low
Max RMSD: 2.8, Avg RMSD: 1.9
PDBFlex
90 % 4 5 15897
70 % 4 5 14842
50 % 4 6 10703
40 % 4 6 9665
30 % 4 6 8287
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 % 105 127 243
95 % 105 127 319 Flexibility: Low
Max RMSD: 6.8, Avg RMSD: 1.6
PDBFlex
90 % 105 127 331
70 % 107 132 357
50 % 108 147 386
40 % 108 147 415
30 % 108 147 412
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 % 105 129 240
95 % 105 129 313 Flexibility: Low
Max RMSD: 3.3, Avg RMSD: 1.2
PDBFlex
90 % 105 129 324
70 % 108 136 343
50 % 108 149 377
40 % 113 157 360
30 % 216 325 139
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 % 103 124 251
95 % 103 124 328 Flexibility: Low
Max RMSD: 1.0, Avg RMSD: 0.5
PDBFlex
90 % 103 124 341
70 % 103 124 385
50 % 103 124 452
40 % 103 124 487
30 % 103 124 490
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 66 624
95 % 51 66 766 Flexibility: Low
Max RMSD: 3.5, Avg RMSD: 0.8
PDBFlex
90 % 51 66 793
70 % 52 69 800
50 % 54 74 767
40 % 54 74 796
30 % 54 74 799
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 % 111 169 184
95 % 111 169 232 Flexibility: Low
Max RMSD: 2.1, Avg RMSD: 0.7
PDBFlex
90 % 111 169 240
70 % 113 174 251
50 % 114 176 270
40 % 114 189 275
30 % 114 189 287
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 % 108 163 189
95 % 108 163 240 Flexibility: Low
Max RMSD: 1.4, Avg RMSD: 0.6
PDBFlex
90 % 108 163 249
70 % 108 163 277
50 % 111 184 251
40 % 111 184 278
30 % 111 184 293
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 69 555
95 % 53 69 694 Flexibility: Low
Max RMSD: 4.4, Avg RMSD: 0.7
PDBFlex
90 % 53 69 721
70 % 53 69 766
50 % 57 90 563
40 % 57 90 608
30 % 57 90 606

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