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 % 109 172 186
95 % 110 173 234 Flexibility: Low
Max RMSD: 1.9, Avg RMSD: 0.9
PDBFlex
90 % 110 173 242
70 % 110 173 269
50 % 112 185 272
40 % 112 185 307
30 % 113 201 286
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 % 104 132 240
95 % 104 132 308 Flexibility: Low
Max RMSD: 2.9, Avg RMSD: 1.0
PDBFlex
90 % 104 132 321
70 % 106 144 338
50 % 107 146 404
40 % 107 146 429
30 % 107 161 400
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 % 110 172 184
95 % 110 172 235 Flexibility: No
Max RMSD: 1.1, Avg RMSD: 0.5
PDBFlex
90 % 110 172 243
70 % 113 199 217
50 % 118 207 227
40 % 118 207 256
30 % 118 207 271
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 % 105 133 238
95 % 105 133 305 Flexibility: No
Max RMSD: 1.1, Avg RMSD: 0.5
PDBFlex
90 % 105 133 318
70 % 105 133 367
50 % 107 145 412
40 % 108 147 427
30 % 108 147 427
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 % 108 168 241 Flexibility: Low
Max RMSD: 2.0, Avg RMSD: 1.0
PDBFlex
90 % 108 168 247
70 % 108 168 282
50 % 110 180 285
40 % 110 180 319
30 % 110 180 327
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 28939
95 % 4 5 15836 Flexibility: Low
Max RMSD: 2.8, Avg RMSD: 1.9
PDBFlex
90 % 4 5 16381
70 % 4 5 15222
50 % 4 6 11002
40 % 4 6 9923
30 % 4 6 8490
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 % 105 131 247
95 % 105 131 316 Flexibility: Low
Max RMSD: 6.8, Avg RMSD: 1.6
PDBFlex
90 % 105 131 328
70 % 107 143 343
50 % 108 158 373
40 % 108 158 403
30 % 108 158 408
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 % 105 133 239
95 % 105 133 306 Flexibility: Low
Max RMSD: 3.3, Avg RMSD: 1.2
PDBFlex
90 % 105 133 319
70 % 108 147 335
50 % 108 160 365
40 % 113 168 364
30 % 219 345 142
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 % 103 128 251
95 % 103 128 325 Flexibility: Low
Max RMSD: 1.0, Avg RMSD: 0.5
PDBFlex
90 % 103 128 337
70 % 103 128 383
50 % 103 128 457
40 % 103 128 494
30 % 103 128 496
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 70 594
95 % 51 70 731 Flexibility: Low
Max RMSD: 3.5, Avg RMSD: 0.8
PDBFlex
90 % 51 70 766
70 % 52 73 771
50 % 54 85 683
40 % 54 85 715
30 % 54 85 722
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 % 111 173 183
95 % 111 173 233 Flexibility: Low
Max RMSD: 2.1, Avg RMSD: 0.7
PDBFlex
90 % 111 173 241
70 % 113 185 243
50 % 114 187 266
40 % 114 200 275
30 % 114 200 289
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 % 108 167 242 Flexibility: Low
Max RMSD: 1.4, Avg RMSD: 0.6
PDBFlex
90 % 108 167 248
70 % 108 167 284
50 % 111 195 250
40 % 111 195 283
30 % 111 195 298
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 73 554
95 % 53 73 681 Flexibility: Low
Max RMSD: 4.4, Avg RMSD: 0.7
PDBFlex
90 % 53 73 706
70 % 53 73 756
50 % 57 101 520
40 % 57 101 568
30 % 57 101 571

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 2.7.7.6 | 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 3H0G 11 K, W DNA-directed RNA polymerase II subunit RPB11 4896
107 3FKI 11 K DNA-directed RNA polymerase II subunit RPB11 4932
108 1Y1Y 13 K DNA-directed RNA polymerase II 13.6 kDa polypeptide 4932 2.7.7.6 | Details
109 1SFO 11 K DNA-directed RNA polymerase II 13.6 kDa polypeptide 4932 2.7.7.6 | Details
110 2E2H 12 K DNA-directed RNA polymerase II 13.6 kDa polypeptide 4932 2.7.7.6 | Details
111 2JA6 11 K DNA-DIRECTED RNA POLYMERASE II 13.6 KDA POLYPEPTIDE 4932 2.7.7.6 | Details
112 2NVZ 12 K DNA-directed RNA polymerase II 13.6 kDa polypeptide 4932 2.7.7.6 | Details
113 1Y77 14 K DNA-directed RNA polymerase II 13.6 kDa polypeptide 4932 2.7.7.6 | Details
114 1NIK 11 K DNA-directed RNA polymerase II, chain RPB11 4932 2.7.7.6 | Details
115 1R9S 11 K DNA-directed RNA polymerase II 13.6 kDa polypeptide 4932 2.7.7.6 | Details
116 1R5U 9 K DNA-directed RNA polymerase II 13.6 kDa polypeptide 4932 2.7.7.6 | Details
117 2B8K 11 K DNA-directed RNA polymerase II 13.6 kDa polypeptide 4932 2.7.7.6 | Details
118 5X51 11 K, W RNA polymerase II subunit B12.5 460519
119 5X4Z 11 K, W RNA polymerase II subunit B12.5 460519
120 6I84 17 K DNA-directed RNA polymerase II subunit RPB11 4932
121 6GYK 11 K DNA-directed RNA polymerase II subunit RPB11 4932
122 6GYL 11 K DNA-directed RNA polymerase II subunit RPB11 4932
123 6GYM 19 K DNA-directed RNA polymerase II subunit RPB11 4932
124 6A5O 11 K RNA polymerase II subunit B12.5 460519
125 6A5P 11 K RNA polymerase II subunit B12.5 460519
126 6A5R 11 K RNA polymerase II subunit B12.5 460519
127 6A5T 11 K RNA polymerase II subunit B12.5 460519
128 6A5U 11 K RNA polymerase II subunit B12.5 460519
129 6A5V 11 K RNA polymerase II subunit B12.5 460519
130 6A5L 11 K RNA polymerase II subunit B12.5 460519
131 5OQM 11 K DNA-directed RNA polymerase II subunit RPB11 4932
132 5OQJ 11 K DNA-directed RNA polymerase II subunit RPB11 4932
133 5XON 11 K RNA polymerase II subunit B12.5 460519
134 5VVS 11 K DNA-directed RNA polymerase II subunit RPB11 4932
135 5VVR 11 K DNA-directed RNA polymerase II subunit RPB11 4932
136 5U0S 27 k RNA polymerase II subunit Rpb11 4896
137 5SVA 11 K DNA-directed RNA polymerase II subunit RPB11 4932
138 5FYW 11 K DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB11 4932
139 5FZ5 11 K DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB11 4932
140 5FMF 13 K DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB11 4932
141 4V1M 9 K DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB11 4932
142 4V1N 11 K DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB11 2.7.7.6 4932
143 4V1O 11 K DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB11 2.7.7.6 4932
144 3J1N 11 K DNA-directed RNA polymerase II subunit RPB11 4932
145 3J0K 11 K DNA-directed RNA polymerase II 13.6 kDa polypeptide 9606 2.7.7.6 | Details
146 1PQV 11 K DNA-directed RNA polymerase II 13.6 kDa polypeptide 4932 2.7.7.6 | Details
147 1NT9 11 K DNA-DIRECTED RNA POLYMERASE II 13.6 KD POLYPEPTIDE 4932 2.7.7.6 | Details