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 % 109 171 185
95 % 110 172 231 Flexibility: Low
Max RMSD: 1.9, Avg RMSD: 0.9
PDBFlex
90 % 110 172 240
70 % 110 172 268
50 % 112 184 266
40 % 112 184 302
30 % 113 200 282
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 % 104 131 240
95 % 104 131 304 Flexibility: Low
Max RMSD: 2.9, Avg RMSD: 1.0
PDBFlex
90 % 104 131 316
70 % 106 143 336
50 % 107 145 398
40 % 107 145 423
30 % 107 160 393
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 % 110 171 184
95 % 110 171 233 Flexibility: No
Max RMSD: 1.1, Avg RMSD: 0.5
PDBFlex
90 % 110 171 242
70 % 113 198 216
50 % 118 206 223
40 % 118 206 252
30 % 118 206 267
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 % 105 132 234
95 % 105 132 301 Flexibility: No
Max RMSD: 1.1, Avg RMSD: 0.5
PDBFlex
90 % 105 132 312
70 % 105 132 362
50 % 107 144 403
40 % 108 146 422
30 % 108 146 420
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 % 108 167 187
95 % 108 167 238 Flexibility: Low
Max RMSD: 2.0, Avg RMSD: 1.0
PDBFlex
90 % 108 167 245
70 % 108 167 280
50 % 110 179 278
40 % 110 179 313
30 % 110 179 321
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 28689
95 % 4 5 15692 Flexibility: Low
Max RMSD: 2.8, Avg RMSD: 1.9
PDBFlex
90 % 4 5 16250
70 % 4 5 15106
50 % 4 6 10927
40 % 4 6 9853
30 % 4 6 8435
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 % 105 130 245
95 % 105 130 313 Flexibility: Low
Max RMSD: 6.8, Avg RMSD: 1.6
PDBFlex
90 % 105 130 326
70 % 107 142 339
50 % 108 157 366
40 % 108 157 399
30 % 108 157 403
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 % 105 132 237
95 % 105 132 302 Flexibility: Low
Max RMSD: 3.3, Avg RMSD: 1.2
PDBFlex
90 % 105 132 313
70 % 108 146 332
50 % 108 159 359
40 % 113 167 357
30 % 216 340 143
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 % 103 127 248
95 % 103 127 323 Flexibility: Low
Max RMSD: 1.0, Avg RMSD: 0.5
PDBFlex
90 % 103 127 336
70 % 103 127 385
50 % 103 127 453
40 % 103 127 491
30 % 103 127 496
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 69 598
95 % 51 69 736 Flexibility: Low
Max RMSD: 3.5, Avg RMSD: 0.8
PDBFlex
90 % 51 69 769
70 % 52 72 781
50 % 54 84 680
40 % 54 84 718
30 % 54 84 722
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 % 111 172 181
95 % 111 172 230 Flexibility: Low
Max RMSD: 2.1, Avg RMSD: 0.7
PDBFlex
90 % 111 172 239
70 % 113 184 241
50 % 114 186 263
40 % 114 199 270
30 % 114 199 284
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 % 108 166 188
95 % 108 166 240 Flexibility: Low
Max RMSD: 1.4, Avg RMSD: 0.6
PDBFlex
90 % 108 166 247
70 % 108 166 283
50 % 111 194 245
40 % 111 194 277
30 % 111 194 291
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 72 551
95 % 53 72 686 Flexibility: Low
Max RMSD: 4.4, Avg RMSD: 0.7
PDBFlex
90 % 53 72 708
70 % 53 72 754
50 % 57 100 519
40 % 57 100 563
30 % 57 100 573

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 9 K DNA-directed RNA polymerase II 13.6 kDa polypeptide 4932 2.3.2.24 | Details
2 3S14 9 K DNA-directed RNA polymerase II subunit RPB11 4932 2.3.2.24 | Details
3 3CQZ 9 K DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB11 4932 2.3.2.24 | Details
4 3PO2 11 K DNA-directed RNA polymerase II subunit RPB11 4932 2.3.2.24 | Details
5 3RZO 9 K DNA-directed RNA polymerase II subunit RPB11 4932 2.3.2.24 | Details
6 3PO3 11 K DNA-directed RNA polymerase II subunit RPB11 4932 2.3.2.24 | Details
7 3S1M 9 K DNA-directed RNA polymerase II subunit RPB11 4932 2.3.2.24 | Details
8 4A3E 11 K DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB11 4932 2.3.2.24 | Details
9 5OT2 11 K DNA-directed RNA polymerase II subunit RPB11 4932 2.3.2.24 | Details
10 3S1R 9 K DNA-directed RNA polymerase II subunit RPB11 4932 2.3.2.24 | Details
11 4A3D 11 K DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB11 4932 2.3.2.24 | Details
12 3S1N 9 K DNA-directed RNA polymerase II subunit RPB11 4932 2.3.2.24 | Details
13 5IP7 11 K DNA-directed RNA polymerase II subunit RPB11 4932 2.3.2.24 | Details
14 4A3F 11 K DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB11 4932 2.3.2.24 | Details
15 4A93 11 K DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB11 4932 2.3.2.24 | Details
16 1K83 9 K DNA-DIRECTED RNA POLYMERASE II 13.6KD POLYPEPTIDE 4932 2.3.2.24 | Details
17 1I50 9 K DNA-DIRECTED RNA POLYMERASE II 13.6KD POLYPEPTIDE 4932 2.3.2.24 | Details
18 4BY7 11 K DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB11 4932 2.3.2.24 | Details
19 3S2D 9 K DNA-directed RNA polymerase II subunit RPB11 4932 2.3.2.24 | Details
20 4A3C 11 K DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB11 4932 2.3.2.24 | Details
21 4A3K 11 K DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB11 4932 2.3.2.24 | Details
22 3S15 9 K DNA-directed RNA polymerase II subunit RPB11 4932 2.3.2.24 | Details
23 4A3L 11 K DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB11 4932 2.3.2.24 | Details
24 4BXX 11 K DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB11 4932 2.3.2.24 | Details
25 3S1Q 9 K DNA-directed RNA polymerase II subunit RPB11 4932 2.3.2.24 | Details
26 3S16 9 K DNA-directed RNA polymerase II subunit RPB11 4932 2.3.2.24 | Details
27 3S17 9 K DNA-directed RNA polymerase II subunit RPB11 4932 2.3.2.24 | Details
28 4A3G 11 K DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB11 4932 2.3.2.24 | Details
29 4A3B 11 K DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB11 4932 2.3.2.24 | Details
30 4BBR 11 K DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB11 4932 2.3.2.24 | Details
31 2NVQ 12 K DNA-directed RNA polymerase II 13.6 kDa polypeptide 4932 2.3.2.24 | Details
32 3RZD 9 K DNA-directed RNA polymerase II subunit RPB11 4932 2.3.2.24 | Details
33 4A3J 11 K DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB11 4932 2.3.2.24 | Details
34 3S2H 9 K DNA-directed RNA polymerase II subunit RPB11 4932 2.3.2.24 | Details
35 3M3Y 9 K DNA-directed RNA polymerase II subunit RPB11 4932 2.3.2.24 | Details
36 4A3I 11 K DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB11 4932 2.3.2.24 | Details
37 6BM4 9 K DNA-directed RNA polymerase II subunit RPB11 4932 2.3.2.24 | Details
38 4BY1 11 K DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB11 4932 2.3.2.24 | Details
39 4A3M 11 K DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB11 4932 2.3.2.24 | Details
40 6BLP 9 K DNA-directed RNA polymerase II subunit RPB11 4932 2.3.2.24 | Details
41 4Y7N 9 K DNA-directed RNA polymerase II subunit RPB11 4932 2.3.2.24 | Details
42 5IP9 11 K DNA-directed RNA polymerase II subunit RPB11 4932 2.3.2.24 | Details
43 1I3Q 9 K DNA-DIRECTED RNA POLYMERASE II 13.6KD POLYPEPTIDE 4932 2.3.2.24 | Details
44 4BBS 11 K DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB11 4932 2.3.2.24 | Details
45 6BLO 9 K DNA-directed RNA polymerase II subunit RPB11 4932 2.3.2.24 | Details
46 1TWC 9 K DNA-directed RNA polymerase II 13.6 kDa polypeptide 4932 2.3.2.24 | Details
47 4Y52 9 K DNA-directed RNA polymerase II subunit RPB11 4932 2.3.2.24 | Details
48 6BQF 9 K DNA-directed RNA polymerase II subunit RPB11 4932 2.3.2.24 | Details
49 3HOU 11 K, W DNA-directed RNA polymerase II subunit RPB11 4932 2.3.2.24 | Details
50 3HOY 11 K DNA-directed RNA polymerase II subunit RPB11 4932 2.3.2.24 | Details
51 3HOV 11 K DNA-directed RNA polymerase II subunit RPB11 4932 2.3.2.24 | Details
52 6BM2 9 K DNA-directed RNA polymerase II subunit RPB11 4932 2.3.2.24 | Details
53 1TWA 9 K DNA-directed RNA polymerase II 13.6 kDa polypeptide 4932 2.3.2.24 | Details
54 5C3E 11 K DNA-directed RNA polymerase II subunit RPB11 4932 2.3.2.24 | Details
55 5W51 9 K DNA-directed RNA polymerase II subunit RPB11 4932 2.3.2.24 | Details
56 2NVT 12 K DNA-directed RNA polymerase II 13.6 kDa polypeptide 4932 2.3.2.24 | Details
57 3HOZ 11 K DNA-directed RNA polymerase II subunit RPB11 4932 2.3.2.24 | Details
58 3HOW 11 K DNA-directed RNA polymerase II subunit RPB11 4932 2.3.2.24 | Details
59 3HOX 11 K DNA-directed RNA polymerase II subunit RPB11 4932 2.3.2.24 | Details
60 1I6H 11 K DNA-DIRECTED RNA POLYMERASE II 13.6KD POLYPEPTIDE 4932 2.3.2.24 | Details
61 2R92 13 K DNA-directed RNA polymerase II subunit RPB11 4932 2.3.2.24 | Details
62 5W4U 9 K DNA-directed RNA polymerase II subunit RPB11 4932 2.3.2.24 | Details
63 2R7Z 14 K DNA-directed RNA polymerase II subunit RPB11 4932 2.3.2.24 | Details
64 1R9T 12 K DNA-directed RNA polymerase II 13.6 kDa polypeptide 4932 2.3.2.24 | Details
65 3I4M 11 K DNA-directed RNA polymerase II subunit RPB11 4932 2.3.2.24 | Details
66 3H3V 11 L DNA-directed RNA polymerase II subunit RPB11 4932 2.3.2.24 | Details
67 5U5Q 11 K DNA-directed RNA polymerase II subunit RPB11 4932 2.3.2.24 | Details
68 1TWH 9 K DNA-directed RNA polymerase II 13.6 kDa polypeptide 4932 2.3.2.24 | Details
69 2NVY 9 K DNA-directed RNA polymerase II 13.6 kDa polypeptide 4932 2.3.2.24 | Details
70 2E2J 12 K DNA-directed RNA polymerase II 13.6 kDa polypeptide 4932 2.3.2.24 | Details
71 5C4X 11 K DNA-directed RNA polymerase II subunit RPB11 4932 2.3.2.24 | Details
72 2VUM 11 K DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB11 4932 2.3.2.24 | Details
73 5C44 11 K DNA-directed RNA polymerase II subunit RPB11 4932 2.3.2.24 | Details
74 3M4O 9 K DNA-directed RNA polymerase II subunit RPB11 4932 2.3.2.24 | Details
75 5C4J 9 K DNA-directed RNA polymerase II subunit RPB11 4932 2.3.2.24 | Details
76 2R93 12 K DNA-directed RNA polymerase II subunit RPB11 4932 2.3.2.24 | Details
77 1TWG 9 K DNA-directed RNA polymerase II 13.6 kDa polypeptide 4932 2.3.2.24 | Details
78 3GTM 9 K DNA-directed RNA polymerase II subunit RPB11 DNA-directed RNA polymerase II 13.6 kDa polypeptide 4932 2.3.2.24 | Details
79 3I4N 11 K DNA-directed RNA polymerase II subunit RPB11 4932 2.3.2.24 | Details
80 2E2I 12 K DNA-directed RNA polymerase II 13.6 kDa polypeptide 4932 2.3.2.24 | Details
81 3GTL 9 K DNA-directed RNA polymerase II subunit RPB11 DNA-directed RNA polymerase II 13.6 kDa polypeptide 4932 2.3.2.24 | Details
82 4BXZ 11 K DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB11 4932 2.3.2.24 | Details
83 3GTK 9 K DNA-directed RNA polymerase II subunit RPB11 DNA-directed RNA polymerase II 13.6 kDa polypeptide 4932 2.3.2.24 | Details
84 5C4A 11 K DNA-directed RNA polymerase II subunit RPB11 4932 2.3.2.24 | Details
85 3K1F 11 K DNA-directed RNA polymerase II subunit RPB11 4932 2.3.2.24 | Details
86 3GTJ 9 K DNA-directed RNA polymerase II subunit RPB11 DNA-directed RNA polymerase II 13.6 kDa polypeptide 4932 2.3.2.24 | Details
87 3GTG 9 K DNA-directed RNA polymerase II subunit RPB11 DNA-directed RNA polymerase II 13.6 kDa polypeptide 4932 2.3.2.24 | Details
88 2YU9 12 K DNA-directed RNA polymerase II 13.6 kDa polypeptide 4932 2.3.2.24 | Details
89 1WCM 11 K DNA-DIRECTED RNA POLYMERASE II 13.6 KDA POLYPEPTIDE 4932 2.3.2.24 | Details
90 2JA7 14 K, W DNA-DIRECTED RNA POLYMERASE II 13.6 KDA POLYPEPTIDE 4932 2.3.2.24 | Details
91 4X6A 9 K DNA-directed RNA polymerase II subunit RPB11 4932 2.3.2.24 | Details
92 4X67 9 K DNA-directed RNA polymerase II subunit RPB11 4932 2.3.2.24 | Details
93 1Y1W 14 K DNA-directed RNA polymerase II 13.6 kDa polypeptide 4932 2.3.2.24 | Details
94 3QT1 11 K DNA-directed RNA polymerase II subunit RPB11 4932 2.3.2.24 | Details
95 3K7A 9 K DNA-directed RNA polymerase II subunit RPB11 4932 2.3.2.24 | Details
96 2JA8 11 K DNA-DIRECTED RNA POLYMERASE II 13.6 KDA POLYPEPTIDE 4932 2.3.2.24 | Details
97 2JA5 11 K DNA-directed RNA polymerase II subunit RPB11 4932 2.3.2.24 | Details
98 2NVX 12 K DNA-directed RNA polymerase II 13.6 kDa polypeptide 4932 2.3.2.24 | Details
99 2B63 12 K DNA-directed RNA polymerase II 13.6 kDa polypeptide 4932 2.3.2.24 | Details
100 3GTQ 9 K DNA-directed RNA polymerase II subunit RPB11 DNA-directed RNA polymerase II 13.6 kDa polypeptide 4932 2.3.2.24 | Details
101 3GTP 9 K DNA-directed RNA polymerase II subunit RPB11 DNA-directed RNA polymerase II 13.6 kDa polypeptide 4932 2.3.2.24 | Details
102 1Y1V 11 K DNA-directed RNA polymerase II 13.6 kDa polypeptide 4932 2.3.2.24 | Details
103 3GTO 9 K DNA-directed RNA polymerase II subunit RPB11 DNA-directed RNA polymerase II 13.6 kDa polypeptide 4932 2.3.2.24 | Details
104 3FKI 11 K DNA-directed RNA polymerase II subunit RPB11 4932 2.3.2.24 | Details
105 1Y1Y 13 K DNA-directed RNA polymerase II 13.6 kDa polypeptide 4932 2.3.2.24 | Details
106 1SFO 11 K DNA-directed RNA polymerase II 13.6 kDa polypeptide 4932 2.3.2.24 | Details
107 2E2H 12 K DNA-directed RNA polymerase II 13.6 kDa polypeptide 4932 2.3.2.24 | Details
108 2JA6 11 K DNA-DIRECTED RNA POLYMERASE II 13.6 KDA POLYPEPTIDE 4932 2.3.2.24 | Details
109 2NVZ 12 K DNA-directed RNA polymerase II 13.6 kDa polypeptide 4932 2.3.2.24 | Details
110 1Y77 14 K DNA-directed RNA polymerase II 13.6 kDa polypeptide 4932 2.3.2.24 | Details
111 1NIK 11 K DNA-directed RNA polymerase II, chain RPB11 4932 2.3.2.24 | Details
112 1R9S 11 K DNA-directed RNA polymerase II 13.6 kDa polypeptide 4932 2.3.2.24 | Details
113 1R5U 9 K DNA-directed RNA polymerase II 13.6 kDa polypeptide 4932 2.3.2.24 | Details
114 2B8K 11 K DNA-directed RNA polymerase II 13.6 kDa polypeptide 4932 2.3.2.24 | Details
115 6GYK 11 K DNA-directed RNA polymerase II subunit RPB11 4932 2.3.2.24 | Details
116 6GYL 11 K DNA-directed RNA polymerase II subunit RPB11 4932 2.3.2.24 | Details
117 6GYM 19 K DNA-directed RNA polymerase II subunit RPB11 4932 2.3.2.24 | Details
118 5OQM 11 K DNA-directed RNA polymerase II subunit RPB11 4932 2.3.2.24 | Details
119 5OQJ 11 K DNA-directed RNA polymerase II subunit RPB11 4932 2.3.2.24 | Details
120 5VVS 11 K DNA-directed RNA polymerase II subunit RPB11 4932 2.3.2.24 | Details
121 5VVR 11 K DNA-directed RNA polymerase II subunit RPB11 4932 2.3.2.24 | Details
122 5SVA 11 K DNA-directed RNA polymerase II subunit RPB11 4932 2.3.2.24 | Details
123 5FYW 11 K DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB11 4932 2.3.2.24 | Details
124 5FZ5 11 K DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB11 4932 2.3.2.24 | Details
125 5FMF 13 K DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB11 4932 2.3.2.24 | Details
126 4V1M 9 K DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB11 4932 2.3.2.24 | Details
127 4V1N 11 K DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB11 2.7.7.6 4932 2.3.2.24 | Details
128 4V1O 11 K DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB11 2.7.7.6 4932 2.3.2.24 | Details
129 3J1N 11 K DNA-directed RNA polymerase II subunit RPB11 4932 2.3.2.24 | Details
130 3J0K 11 K DNA-directed RNA polymerase II 13.6 kDa polypeptide 9606 2.3.2.24 | Details
131 1PQV 11 K DNA-directed RNA polymerase II 13.6 kDa polypeptide 4932 2.3.2.24 | Details
132 1NT9 11 K DNA-DIRECTED RNA POLYMERASE II 13.6 KD POLYPEPTIDE 4932 2.3.2.24 | Details