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.

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Rank PDB ID Entity ID Chains Description Details Taxonomy EC Number
1 1TWF 2 B DNA-directed RNA polymerase II 140 kDa polypeptide 4932 2.7.7.6 | Details
2 3S14 2 B DNA-directed RNA polymerase II subunit RPB2 4932 2.7.7.6 | Details
3 3CQZ 2 B DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB2 4932 2.7.7.6 | Details
4 3PO2 2 B DNA-directed RNA polymerase II subunit RPB2 4932 2.7.7.6 | Details
5 3RZO 2 B DNA-directed RNA polymerase II subunit RPB2 4932 2.7.7.6 | Details
6 3PO3 2 B DNA-directed RNA polymerase II subunit RPB2 4932 2.7.7.6 | Details
7 3S1M 2 B DNA-directed RNA polymerase II subunit RPB2 4932 2.7.7.6 | Details
8 4A3E 2 B DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB2 4932 2.7.7.6 | Details
9 5OT2 2 B DNA-directed RNA polymerase II subunit RPB2 4932 2.7.7.6 | Details
10 3S1R 2 B DNA-directed RNA polymerase II subunit RPB2 4932 2.7.7.6 | Details
11 4A3D 2 B DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB2 4932 2.7.7.6 | Details
12 3S1N 2 B DNA-directed RNA polymerase II subunit RPB2 4932 2.7.7.6 | Details
13 5IP7 2 B DNA-directed RNA polymerase II subunit RPB2 4932 2.7.7.6 | Details
14 4A3F 2 B DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB2 4932 2.7.7.6 | Details
15 4A93 2 B DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB2 4932 2.7.7.6 | Details
16 1K83 2 B DNA-DIRECTED RNA POLYMERASE II 140KD POLYPEPTIDE 4932 2.7.7.6 | Details
17 1I50 2 B DNA-DIRECTED RNA POLYMERASE II 140KD POLYPEPTIDE 4932 2.7.7.6 | Details
18 4BY7 2 B DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB2 4932 2.7.7.6 | Details
19 3S2D 2 B DNA-directed RNA polymerase II subunit RPB2 4932 2.7.7.6 | Details
20 4A3C 2 B DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB2 4932 2.7.7.6 | Details
21 4A3K 2 B DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB2 4932 2.7.7.6 | Details
22 3S15 2 B DNA-directed RNA polymerase II subunit RPB2 4932 2.7.7.6 | Details
23 4A3L 2 B DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB2 4932 2.7.7.6 | Details
24 4BXX 2 B DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB2 4932 2.7.7.6 | Details
25 3S1Q 2 B DNA-directed RNA polymerase II subunit RPB2 4932 2.7.7.6 | Details
26 3S16 2 B DNA-directed RNA polymerase II subunit RPB2 4932 2.7.7.6 | Details
27 3S17 2 B DNA-directed RNA polymerase II subunit RPB2 4932 2.7.7.6 | Details
28 4A3G 2 B DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB2 4932 2.7.7.6 | Details
29 4A3B 2 B DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB2 4932 2.7.7.6 | Details
30 4BBR 2 B DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB2 4932 2.7.7.6 | Details
31 2NVQ 5 B DNA-directed RNA polymerase II 140 kDa polypeptide 4932 2.7.7.6 | Details
32 3RZD 2 B DNA-directed RNA polymerase II subunit RPB2 4932 2.7.7.6 | Details
33 4A3J 2 B DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB2 4932 2.7.7.6 | Details
34 3S2H 2 B DNA-directed RNA polymerase II subunit RPB2 4932 2.7.7.6 | Details
35 3M3Y 2 B DNA-directed RNA polymerase II subunit RPB2 4932 2.7.7.6 | Details
36 4A3I 2 B DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB2 4932 2.7.7.6 | Details
37 6BM4 2 B DNA-directed RNA polymerase II subunit RPB2 4932 2.7.7.6 | Details
38 4BY1 2 B DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB2 4932 2.7.7.6 | Details
39 4A3M 2 B DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB2 4932 2.7.7.6 | Details
40 6BLP 2 B DNA-directed RNA polymerase II subunit RPB2 4932 2.7.7.6 | Details
41 4Y7N 2 B DNA-directed RNA polymerase II subunit RPB2,DNA-directed RNA polymerase II subunit RPB2 4932 2.7.7.6 | Details
42 5IP9 2 B DNA-directed RNA polymerase II subunit RPB2 4932 2.7.7.6 | Details
43 1I3Q 2 B DNA-DIRECTED RNA POLYMERASE II 140KD POLYPEPTIDE 4932 2.7.7.6 | Details
44 4BBS 2 B DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB2 4932 2.7.7.6 | Details
45 6BLO 2 B DNA-directed RNA polymerase II subunit RPB2 4932 2.7.7.6 | Details
46 1TWC 2 B DNA-directed RNA polymerase II 140 kDa polypeptide 4932 2.7.7.6 | Details
47 4Y52 2 B DNA-directed RNA polymerase II subunit RPB2 4932 2.7.7.6 | Details
48 6BQF 2 B DNA-directed RNA polymerase II subunit RPB2 4932 2.7.7.6 | Details
49 3HOU 2 B, N DNA-directed RNA polymerase II subunit RPB2 4932 2.7.7.6 | Details
50 3HOY 2 B DNA-directed RNA polymerase II subunit RPB2 4932 2.7.7.6 | Details
51 3HOV 2 B DNA-directed RNA polymerase II subunit RPB2 4932 2.7.7.6 | Details
52 6BM2 2 B DNA-directed RNA polymerase II subunit RPB2 4932 2.7.7.6 | Details
53 1TWA 2 B DNA-directed RNA polymerase II 140 kDa polypeptide 4932 2.7.7.6 | Details
54 5C3E 2 B DNA-directed RNA polymerase II subunit RPB2 4932 2.7.7.6 | Details
55 5W51 2 B DNA-directed RNA polymerase II subunit RPB2 4932 2.7.7.6 | Details
56 2NVT 5 B DNA-directed RNA polymerase II 140 kDa polypeptide 4932 2.7.7.6 | Details
57 3HOZ 2 B DNA-directed RNA polymerase II subunit RPB2 4932 2.7.7.6 | Details
58 3HOW 2 B DNA-directed RNA polymerase II subunit RPB2 4932 2.7.7.6 | Details
59 3HOX 2 B DNA-directed RNA polymerase II subunit RPB2 4932 2.7.7.6 | Details
60 1I6H 4 B DNA-DIRECTED RNA POLYMERASE II 140KD POLYPEPTIDE 4932 2.7.7.6 | Details
61 2R92 4 B DNA-directed RNA polymerase II subunit RPB2 4932 2.7.7.6 | Details
62 5W4U 2 B DNA-directed RNA polymerase II subunit RPB2 4932 2.7.7.6 | Details
63 2R7Z 5 B DNA-directed RNA polymerase II subunit RPB2 4932 2.7.7.6 | Details
64 1R9T 5 B DNA-directed RNA polymerase II 140 kDa polypeptide 4932 2.7.7.6 | Details
65 3I4M 2 B DNA-directed RNA polymerase II subunit RPB2 4932 2.7.7.6 | Details
66 3H3V 2 C DNA-directed RNA polymerase II subunit RPB2 4932 2.7.7.6 | Details
67 5U5Q 2 B DNA-directed RNA polymerase II subunit RPB2 4932 2.7.7.6 | Details
68 1TWH 2 B DNA-directed RNA polymerase II 140 kDa polypeptide 4932 2.7.7.6 | Details
69 2NVY 2 B DNA-directed RNA polymerase II 140 kDa polypeptide 4932 2.7.7.6 | Details
70 2E2J 5 B DNA-directed RNA polymerase II 140 kDa polypeptide 4932 2.7.7.6 | Details
71 5C4X 2 B DNA-directed RNA polymerase II subunit RPB2 4932 2.7.7.6 | Details
72 2VUM 2 B DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB2 4932 2.7.7.6 | Details
73 5C44 2 B DNA-directed RNA polymerase II subunit RPB2 4932 2.7.7.6 | Details
74 3M4O 2 B DNA-directed RNA polymerase II subunit RPB2 4932 2.7.7.6 | Details
75 5C4J 2 B DNA-directed RNA polymerase II subunit RPB2 4932 2.7.7.6 | Details
76 2R93 3 B DNA-directed RNA polymerase II subunit RPB2 4932 2.7.7.6 | Details
77 1TWG 2 B DNA-directed RNA polymerase II 140 kDa polypeptide 4932 2.7.7.6 | Details
78 3GTM 2 B DNA-directed RNA polymerase II subunit RPB2 DNA-directed RNA polymerase II 140 kDa polypeptide 4932 2.7.7.6 | Details
79 3I4N 2 B DNA-directed RNA polymerase II subunit RPB2 4932 2.7.7.6 | Details
80 2E2I 5 B DNA-directed RNA polymerase II 140 kDa polypeptide 4932 2.7.7.6 | Details
81 3GTL 2 B DNA-directed RNA polymerase II subunit RPB2 DNA-directed RNA polymerase II 140 kDa polypeptide 4932 2.7.7.6 | Details
82 4BXZ 2 B DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB2 4932 2.7.7.6 | Details
83 3GTK 2 B DNA-directed RNA polymerase II subunit RPB2 DNA-directed RNA polymerase II 140 kDa polypeptide 4932 2.7.7.6 | Details
84 5C4A 2 B DNA-directed RNA polymerase II subunit RPB2 4932 2.7.7.6 | Details
85 3K1F 2 B DNA-directed RNA polymerase II subunit RPB2 4932 2.7.7.6 | Details
86 3GTJ 2 B DNA-directed RNA polymerase II subunit RPB2 DNA-directed RNA polymerase II 140 kDa polypeptide 4932 2.7.7.6 | Details
87 3GTG 2 B DNA-directed RNA polymerase II subunit RPB2 DNA-directed RNA polymerase II 140 kDa polypeptide 4932 2.7.7.6 | Details
88 2YU9 5 B DNA-directed RNA polymerase II 140 kDa polypeptide 4932 2.7.7.6 | Details
89 1WCM 2 B DNA-DIRECTED RNA POLYMERASE II SECOND LARGEST SUBUNIT 4932 2.7.7.6 | Details
90 2JA7 5 B, N DNA-DIRECTED RNA POLYMERASE II 140 KDA POLYPEPTIDE 4932 2.7.7.6 | Details
91 4X6A 2 B DNA-directed RNA polymerase II subunit RPB2 4932 2.7.7.6 | Details
92 4X67 2 B DNA-directed RNA polymerase II subunit RPB2 4932 2.7.7.6 | Details
93 1Y1W 5 B DNA-directed RNA polymerase II 140 kDa polypeptide 4932 2.7.7.6 | Details
94 3QT1 2 B DNA-directed RNA polymerase II subunit RPB2 4932 2.7.7.6 | Details
95 3K7A 2 B DNA-directed RNA polymerase II subunit RPB2 4932 2.7.7.6 | Details
96 2JA8 2 B DNA-DIRECTED RNA POLYMERASE II 140 KDA POLYPEPTIDE 4932 2.7.7.6 | Details
97 2JA5 2 B DNA-directed RNA polymerase II subunit RPB2 4932 2.7.7.6 | Details
98 2NVX 5 B DNA-directed RNA polymerase II 140 kDa polypeptide 4932 2.7.7.6 | Details
99 2B63 3 B DNA-directed RNA polymerase II 140 kDa polypeptide 4932 2.7.7.6 | Details
100 3GTQ 2 B DNA-directed RNA polymerase II subunit RPB2 DNA-directed RNA polymerase II 140 kDa polypeptide 4932 2.7.7.6 | Details
101 3GTP 2 B DNA-directed RNA polymerase II subunit RPB2 DNA-directed RNA polymerase II 140 kDa polypeptide 4932 2.7.7.6 | Details
102 1Y1V 2 B DNA-directed RNA polymerase II 140 kDa polypeptide 4932 2.7.7.6 | Details
103 3GTO 2 B DNA-directed RNA polymerase II subunit RPB2 DNA-directed RNA polymerase II 140 kDa polypeptide 4932 2.7.7.6 | Details
104 3FKI 2 B DNA-directed RNA polymerase II subunit RPB2 4932 2.7.7.6 | Details
105 1Y1Y 4 B DNA-directed RNA polymerase II 140 kDa polypeptide 4932 2.7.7.6 | Details
106 1SFO 4 B DNA-directed RNA polymerase II 140 kDa polypeptide 4932 2.7.7.6 | Details
107 2E2H 5 B DNA-directed RNA polymerase II 140 kDa polypeptide 4932 2.7.7.6 | Details
108 2JA6 2 B DNA-DIRECTED RNA POLYMERASE II 140 KDA POLYPEPTIDE 4932 2.7.7.6 | Details
109 2NVZ 5 B DNA-directed RNA polymerase II 140 kDa polypeptide 4932 2.7.7.6 | Details
110 1Y77 5 B DNA-directed RNA polymerase II 140 kDa polypeptide 4932 2.7.7.6 | Details
111 1NIK 2 B ORF YOR151c 4932 2.7.7.6 | Details
112 1R9S 4 B DNA-directed RNA polymerase II 140 kDa polypeptide 4932 2.7.7.6 | Details
113 1R5U 2 B DNA-directed RNA polymerase II 140 kDa polypeptide 4932 2.7.7.6 | Details
114 2B8K 2 B DNA-directed RNA polymerase II 140 kDa polypeptide 4932 2.7.7.6 | Details
115 5OQM 2 B DNA-directed RNA polymerase II subunit RPB2 4932 2.7.7.6 | Details
116 5OQJ 2 B DNA-directed RNA polymerase II subunit RPB2 4932 2.7.7.6 | Details
117 5VVS 2 B DNA-directed RNA polymerase II subunit RPB2 4932 2.7.7.6 | Details
118 5VVR 2 B DNA-directed RNA polymerase II subunit RPB2 4932 2.7.7.6 | Details
119 5SVA 2 B DNA-directed RNA polymerase II subunit RPB2 4932 2.7.7.6 | Details
120 5FYW 2 B DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB2 4932 2.7.7.6 | Details
121 5FZ5 2 B DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB2 4932 2.7.7.6 | Details
122 5FMF 4 B DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB2 4932 2.7.7.6 | Details
123 4V1M 2 B DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB2 4932 2.7.7.6 | Details
124 4V1N 2 B DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB2 4932 2.7.7.6 | Details
125 4V1O 2 B DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB2 4932 2.7.7.6 | Details
126 3J1N 2 B DNA-directed RNA polymerase II subunit RPB2 4932 2.7.7.6 | Details
127 3J0K 2 B DNA-directed RNA polymerase II 140 kDa polypeptide 9606 2.7.7.6 | Details
128 1PQV 2 B DNA-directed RNA polymerase II 140 kDa polypeptide 4932 2.7.7.6 | Details
129 1NT9 2 B DNA-directed polymerase II SECOND LARGEST SUBUNIT 4932 2.7.7.6 | Details