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


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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 5XOG 11 K RNA polymerase II subunit B12.5 460519
8 3S1M 9 K DNA-directed RNA polymerase II subunit RPB11 4932
9 4A3E 11 K DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB11 4932
10 5OT2 11 K DNA-directed RNA polymerase II subunit RPB11 4932
11 3S1R 9 K DNA-directed RNA polymerase II subunit RPB11 4932
12 4A3D 11 K DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB11 4932
13 3S1N 9 K DNA-directed RNA polymerase II subunit RPB11 4932
14 5IP7 11 K DNA-directed RNA polymerase II subunit RPB11 4932
15 4A3F 11 K DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB11 4932
16 4A93 11 K DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB11 4932
17 1K83 9 K DNA-DIRECTED RNA POLYMERASE II 13.6KD POLYPEPTIDE 4932 2.7.7.6 | Details
18 1I50 9 K DNA-DIRECTED RNA POLYMERASE II 13.6KD POLYPEPTIDE 4932 2.7.7.6 | Details
19 4BY7 11 K DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB11 4932
20 3S2D 9 K DNA-directed RNA polymerase II subunit RPB11 4932
21 4A3C 11 K DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB11 4932
22 4A3K 11 K DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB11 4932
23 3S15 9 K DNA-directed RNA polymerase II subunit RPB11 4932
24 4A3L 11 K DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB11 4932
25 4BXX 11 K DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB11 4932
26 3S1Q 9 K DNA-directed RNA polymerase II subunit RPB11 4932
27 3S16 9 K DNA-directed RNA polymerase II subunit RPB11 4932
28 3S17 9 K DNA-directed RNA polymerase II subunit RPB11 4932
29 4A3G 11 K DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB11 4932
30 4A3B 11 K DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB11 4932
31 4BBR 11 K DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB11 4932
32 2NVQ 12 K DNA-directed RNA polymerase II 13.6 kDa polypeptide 4932 2.7.7.6 | Details
33 3RZD 9 K DNA-directed RNA polymerase II subunit RPB11 4932
34 4A3J 11 K DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB11 4932
35 3S2H 9 K DNA-directed RNA polymerase II subunit RPB11 4932
36 3M3Y 9 K DNA-directed RNA polymerase II subunit RPB11 4932
37 4A3I 11 K DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB11 4932
38 6BM4 9 K DNA-directed RNA polymerase II subunit RPB11 4932
39 4BY1 11 K DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB11 4932
40 4A3M 11 K DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB11 4932
41 6BLP 9 K DNA-directed RNA polymerase II subunit RPB11 4932
42 4Y7N 9 K DNA-directed RNA polymerase II subunit RPB11 4932
43 5IP9 11 K DNA-directed RNA polymerase II subunit RPB11 4932
44 1I3Q 9 K DNA-DIRECTED RNA POLYMERASE II 13.6KD POLYPEPTIDE 4932 2.7.7.6 | Details
45 4BBS 11 K DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB11 4932
46 6BLO 9 K DNA-directed RNA polymerase II subunit RPB11 4932
47 1TWC 9 K DNA-directed RNA polymerase II 13.6 kDa polypeptide 4932 2.7.7.6 | Details
48 4Y52 9 K DNA-directed RNA polymerase II subunit RPB11 4932
49 6BQF 9 K DNA-directed RNA polymerase II subunit RPB11 4932
50 3HOU 11 K, W DNA-directed RNA polymerase II subunit RPB11 4932 2.7.7.6 | Details
51 3HOY 11 K DNA-directed RNA polymerase II subunit RPB11 4932 2.7.7.6 | Details
52 3HOV 11 K DNA-directed RNA polymerase II subunit RPB11 4932 2.7.7.6 | Details
53 6BM2 9 K DNA-directed RNA polymerase II subunit RPB11 4932
54 1TWA 9 K DNA-directed RNA polymerase II 13.6 kDa polypeptide 4932 2.7.7.6 | Details
55 5C3E 11 K DNA-directed RNA polymerase II subunit RPB11 4932
56 5W51 9 K DNA-directed RNA polymerase II subunit RPB11 4932
57 2NVT 12 K DNA-directed RNA polymerase II 13.6 kDa polypeptide 4932 2.7.7.6 | Details
58 3HOZ 11 K DNA-directed RNA polymerase II subunit RPB11 4932 2.7.7.6 | Details
59 3HOW 11 K DNA-directed RNA polymerase II subunit RPB11 4932 2.7.7.6 | Details
60 3HOX 11 K DNA-directed RNA polymerase II subunit RPB11 4932 2.7.7.6 | Details
61 1I6H 11 K DNA-DIRECTED RNA POLYMERASE II 13.6KD POLYPEPTIDE 4932 2.7.7.6 | Details
62 2R92 13 K DNA-directed RNA polymerase II subunit RPB11 4932 2.7.7.6 | Details
63 5W4U 9 K DNA-directed RNA polymerase II subunit RPB11 4932
64 2R7Z 14 K DNA-directed RNA polymerase II subunit RPB11 4932 2.7.7.6 | Details
65 1R9T 12 K DNA-directed RNA polymerase II 13.6 kDa polypeptide 4932 2.7.7.6 | Details
66 3I4M 11 K DNA-directed RNA polymerase II subunit RPB11 4932
67 3H3V 11 L DNA-directed RNA polymerase II subunit RPB11 4932 2.7.7.6 | Details
68 5U5Q 11 K DNA-directed RNA polymerase II subunit RPB11 4932
69 1TWH 9 K DNA-directed RNA polymerase II 13.6 kDa polypeptide 4932 2.7.7.6 | Details
70 2NVY 9 K DNA-directed RNA polymerase II 13.6 kDa polypeptide 4932 2.7.7.6 | Details
71 2E2J 12 K DNA-directed RNA polymerase II 13.6 kDa polypeptide 4932 2.7.7.6 | Details
72 5C4X 11 K DNA-directed RNA polymerase II subunit RPB11 4932
73 2VUM 11 K DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB11 4932 2.7.7.6 | Details
74 5C44 11 K DNA-directed RNA polymerase II subunit RPB11 4932
75 3M4O 9 K DNA-directed RNA polymerase II subunit RPB11 4932
76 5C4J 9 K DNA-directed RNA polymerase II subunit RPB11 4932
77 2R93 12 K DNA-directed RNA polymerase II subunit RPB11 4932 2.7.7.6 | Details
78 1TWG 9 K DNA-directed RNA polymerase II 13.6 kDa polypeptide 4932 2.7.7.6 | Details
79 3GTM 9 K DNA-directed RNA polymerase II subunit RPB11 DNA-directed RNA polymerase II 13.6 kDa polypeptide 4932
80 3I4N 11 K DNA-directed RNA polymerase II subunit RPB11 4932
81 2E2I 12 K DNA-directed RNA polymerase II 13.6 kDa polypeptide 4932 2.7.7.6 | Details
82 3GTL 9 K DNA-directed RNA polymerase II subunit RPB11 DNA-directed RNA polymerase II 13.6 kDa polypeptide 4932
83 4BXZ 11 K DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB11 4932 2.7.7.6 | Details
84 3GTK 9 K DNA-directed RNA polymerase II subunit RPB11 DNA-directed RNA polymerase II 13.6 kDa polypeptide 4932
85 5C4A 11 K DNA-directed RNA polymerase II subunit RPB11 4932
86 3K1F 11 K DNA-directed RNA polymerase II subunit RPB11 4932 2.7.7.6 | Details
87 3GTJ 9 K DNA-directed RNA polymerase II subunit RPB11 DNA-directed RNA polymerase II 13.6 kDa polypeptide 4932
88 3GTG 9 K DNA-directed RNA polymerase II subunit RPB11 DNA-directed RNA polymerase II 13.6 kDa polypeptide 4932
89 2YU9 12 K DNA-directed RNA polymerase II 13.6 kDa polypeptide 4932 2.7.7.6 | Details
90 1WCM 11 K DNA-DIRECTED RNA POLYMERASE II 13.6 KDA POLYPEPTIDE 4932 2.7.7.6 | Details
91 2JA7 14 K, W DNA-DIRECTED RNA POLYMERASE II 13.6 KDA POLYPEPTIDE 4932 2.7.7.6 | Details
92 4X6A 9 K DNA-directed RNA polymerase II subunit RPB11 4932
93 4X67 9 K DNA-directed RNA polymerase II subunit RPB11 4932
94 1Y1W 14 K DNA-directed RNA polymerase II 13.6 kDa polypeptide 4932 2.7.7.6 | Details
95 3QT1 11 K DNA-directed RNA polymerase II subunit RPB11 4932 2.7.7.6 | Details
96 3K7A 9 K DNA-directed RNA polymerase II subunit RPB11 4932
97 5X50 11 K RNA polymerase II subunit B12.5 460519
98 2JA8 11 K DNA-DIRECTED RNA POLYMERASE II 13.6 KDA POLYPEPTIDE 4932 2.7.7.6 | Details
99 2JA5 11 K DNA-directed RNA polymerase II subunit RPB11 4932
100 2NVX 12 K DNA-directed RNA polymerase II 13.6 kDa polypeptide 4932 2.7.7.6 | Details
101 2B63 12 K DNA-directed RNA polymerase II 13.6 kDa polypeptide 4932 2.7.7.6 | Details
102 3GTQ 9 K DNA-directed RNA polymerase II subunit RPB11 DNA-directed RNA polymerase II 13.6 kDa polypeptide 4932
103 3GTP 9 K DNA-directed RNA polymerase II subunit RPB11 DNA-directed RNA polymerase II 13.6 kDa polypeptide 4932
104 1Y1V 11 K DNA-directed RNA polymerase II 13.6 kDa polypeptide 4932 2.7.7.6 | Details
105 3GTO 9 K DNA-directed RNA polymerase II subunit RPB11 DNA-directed RNA polymerase II 13.6 kDa polypeptide 4932
106 3FKI 11 K DNA-directed RNA polymerase II subunit RPB11 4932
107 1Y1Y 13 K DNA-directed RNA polymerase II 13.6 kDa polypeptide 4932 2.7.7.6 | Details
108 1SFO 11 K DNA-directed RNA polymerase II 13.6 kDa polypeptide 4932 2.7.7.6 | Details
109 2E2H 12 K DNA-directed RNA polymerase II 13.6 kDa polypeptide 4932 2.7.7.6 | Details
110 2JA6 11 K DNA-DIRECTED RNA POLYMERASE II 13.6 KDA POLYPEPTIDE 4932 2.7.7.6 | Details
111 2NVZ 12 K DNA-directed RNA polymerase II 13.6 kDa polypeptide 4932 2.7.7.6 | Details
112 1Y77 14 K DNA-directed RNA polymerase II 13.6 kDa polypeptide 4932 2.7.7.6 | Details
113 1NIK 11 K DNA-directed RNA polymerase II, chain RPB11 4932 2.7.7.6 | Details
114 1R9S 11 K DNA-directed RNA polymerase II 13.6 kDa polypeptide 4932 2.7.7.6 | Details
115 1R5U 9 K DNA-directed RNA polymerase II 13.6 kDa polypeptide 4932 2.7.7.6 | Details
116 2B8K 11 K DNA-directed RNA polymerase II 13.6 kDa polypeptide 4932 2.7.7.6 | Details
117 5X51 11 K, W RNA polymerase II subunit B12.5 460519
118 5X4Z 11 K, W RNA polymerase II subunit B12.5 460519
119 6J4W 11 K RNA polymerase II subunit B12.5 460519
120 6J4X 11 K RNA polymerase II subunit B12.5 460519
121 6J4Y 11 K RNA polymerase II subunit B12.5 460519
122 6J4Z 11 K RNA polymerase II subunit B12.5 460519
123 6J50 11 K RNA polymerase II subunit B12.5 460519
124 6J51 11 K RNA polymerase II subunit B12.5 460519
125 6I84 17 K DNA-directed RNA polymerase II subunit RPB11 4932
126 6IR9 11 K RNA polymerase II subunit B12.5 460519
127 6GYK 11 K DNA-directed RNA polymerase II subunit RPB11 4932
128 6GYL 11 K DNA-directed RNA polymerase II subunit RPB11 4932
129 6GYM 19 K DNA-directed RNA polymerase II subunit RPB11 4932
130 6A5O 11 K RNA polymerase II subunit B12.5 460519
131 6A5P 11 K RNA polymerase II subunit B12.5 460519
132 6A5R 11 K RNA polymerase II subunit B12.5 460519
133 6A5T 11 K RNA polymerase II subunit B12.5 460519
134 6A5U 11 K RNA polymerase II subunit B12.5 460519
135 6A5V 11 K RNA polymerase II subunit B12.5 460519
136 6A5L 11 K RNA polymerase II subunit B12.5 460519
137 5OQM 11 K DNA-directed RNA polymerase II subunit RPB11 4932
138 5OQJ 11 K DNA-directed RNA polymerase II subunit RPB11 4932
139 5XON 11 K RNA polymerase II subunit B12.5 460519
140 5VVS 11 K DNA-directed RNA polymerase II subunit RPB11 4932
141 5VVR 11 K DNA-directed RNA polymerase II subunit RPB11 4932
142 5SVA 11 K DNA-directed RNA polymerase II subunit RPB11 4932
143 5FYW 11 K DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB11 4932
144 5FZ5 11 K DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB11 4932
145 5FMF 13 K DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB11 4932
146 4V1M 9 K DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB11 4932
147 4V1N 11 K DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB11 2.7.7.6 4932
148 4V1O 11 K DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB11 2.7.7.6 4932
149 3J1N 11 K DNA-directed RNA polymerase II subunit RPB11 4932
150 3J0K 11 K DNA-directed RNA polymerase II 13.6 kDa polypeptide 9606 2.7.7.6 | Details
151 1PQV 11 K DNA-directed RNA polymerase II 13.6 kDa polypeptide 4932 2.7.7.6 | Details
152 1NT9 11 K DNA-DIRECTED RNA POLYMERASE II 13.6 KD POLYPEPTIDE 4932 2.7.7.6 | Details