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 % 109 162 185
95 % 110 163 235 Flexibility: Low
Max RMSD: 1.9, Avg RMSD: 0.9
PDBFlex
90 % 110 163 242
70 % 110 163 275
50 % 112 168 285
40 % 112 168 317
30 % 113 182 289
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 % 104 128 235
95 % 104 128 308 Flexibility: Low
Max RMSD: 2.9, Avg RMSD: 1.0
PDBFlex
90 % 104 128 319
70 % 106 133 345
50 % 107 135 407
40 % 107 135 431
30 % 107 146 404
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 % 110 162 184
95 % 110 162 236 Flexibility: No
Max RMSD: 1.1, Avg RMSD: 0.5
PDBFlex
90 % 110 162 243
70 % 113 180 231
50 % 118 188 232
40 % 118 188 256
30 % 118 188 274
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 % 105 129 233
95 % 105 129 301 Flexibility: No
Max RMSD: 1.1, Avg RMSD: 0.5
PDBFlex
90 % 105 129 313
70 % 105 129 363
50 % 107 134 410
40 % 108 136 427
30 % 108 136 429
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 % 108 158 186
95 % 108 158 242 Flexibility: Low
Max RMSD: 2.0, Avg RMSD: 1.0
PDBFlex
90 % 108 158 249
70 % 108 158 281
50 % 110 163 301
40 % 110 163 332
30 % 110 163 338
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 27551
95 % 4 5 15030 Flexibility: Low
Max RMSD: 2.8, Avg RMSD: 1.9
PDBFlex
90 % 4 5 15569
70 % 4 5 14559
50 % 4 6 10526
40 % 4 6 9501
30 % 4 6 8146
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 % 105 127 237
95 % 105 127 313 Flexibility: Low
Max RMSD: 6.8, Avg RMSD: 1.6
PDBFlex
90 % 105 127 325
70 % 107 132 349
50 % 108 145 385
40 % 108 145 408
30 % 108 145 405
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 % 105 129 234
95 % 105 129 307 Flexibility: Low
Max RMSD: 3.3, Avg RMSD: 1.2
PDBFlex
90 % 105 129 318
70 % 108 136 336
50 % 108 147 377
40 % 113 155 361
30 % 211 311 142
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 % 103 124 245
95 % 103 124 323 Flexibility: Low
Max RMSD: 1.0, Avg RMSD: 0.5
PDBFlex
90 % 103 124 334
70 % 103 124 378
50 % 103 124 447
40 % 103 124 479
30 % 103 124 484
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 66 604
95 % 51 66 742 Flexibility: Low
Max RMSD: 3.5, Avg RMSD: 0.8
PDBFlex
90 % 51 66 767
70 % 52 69 771
50 % 54 74 750
40 % 54 74 782
30 % 54 74 789
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 % 111 163 183
95 % 111 163 233 Flexibility: Low
Max RMSD: 2.1, Avg RMSD: 0.7
PDBFlex
90 % 111 163 240
70 % 113 168 255
50 % 114 170 275
40 % 114 181 278
30 % 114 181 294
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 % 108 157 187
95 % 108 157 243 Flexibility: Low
Max RMSD: 1.4, Avg RMSD: 0.6
PDBFlex
90 % 108 157 250
70 % 108 157 284
50 % 111 176 262
40 % 111 176 288
30 % 111 176 300
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 69 543
95 % 53 69 675 Flexibility: Low
Max RMSD: 4.4, Avg RMSD: 0.7
PDBFlex
90 % 53 69 700
70 % 53 69 745
50 % 57 88 565
40 % 57 88 605
30 % 57 88 608

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 7 I DNA-directed RNA polymerase II 14.2 kDa polypeptide 4932 2.7.7.6 | Details
2 3S14 7 I DNA-directed RNA polymerase II subunit RPB9 4932
3 3CQZ 7 I DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB9 4932
4 3PO2 9 I DNA-directed RNA polymerase II subunit RPB9 4932 2.7.7.6 | Details
5 3RZO 7 I DNA-directed RNA polymerase II subunit RPB9 4932
6 3PO3 9 I DNA-directed RNA polymerase II subunit RPB9 4932 2.7.7.6 | Details
7 5XOG 9 I DNA-directed RNA polymerase subunit 460519
8 3S1M 7 I DNA-directed RNA polymerase II subunit RPB9 4932
9 4A3E 9 I DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB9 4932
10 5OT2 9 I DNA-directed RNA polymerase II subunit RPB9 4932
11 3S1R 7 I DNA-directed RNA polymerase II subunit RPB9 4932
12 4A3D 9 I DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB9 4932
13 3S1N 7 I DNA-directed RNA polymerase II subunit RPB9 4932
14 5IP7 9 I DNA-directed RNA polymerase II subunit RPB9 4932
15 4A3F 9 I DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB9 4932
16 4A93 9 I DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB9 4932
17 1K83 7 I DNA-DIRECTED RNA POLYMERASE II 14.2KD POLYPEPTIDE 4932 2.7.7.6 | Details
18 1I50 7 I DNA-DIRECTED RNA POLYMERASE II 14.2KD POLYPEPTIDE 4932 2.7.7.6 | Details
19 4BY7 9 I DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB9 4932
20 3S2D 7 I DNA-directed RNA polymerase II subunit RPB9 4932
21 4A3C 9 I DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB9 4932
22 4A3K 9 I DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB9 4932
23 3S15 7 I DNA-directed RNA polymerase II subunit RPB9 4932
24 4A3L 9 I DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB9 4932
25 4BXX 9 I DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB9 4932
26 3S1Q 7 I DNA-directed RNA polymerase II subunit RPB9 4932
27 3S16 7 I DNA-directed RNA polymerase II subunit RPB9 4932
28 3S17 7 I DNA-directed RNA polymerase II subunit RPB9 4932
29 4A3G 9 I DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB9 4932
30 4A3B 9 I DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB9 4932
31 4BBR 9 I DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB9 4932
32 2NVQ 10 I DNA-directed RNA polymerase II subunit 9 4932 2.7.7.6 | Details
33 3RZD 7 I DNA-directed RNA polymerase II subunit RPB9 4932
34 4A3J 9 I DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB9 4932
35 3S2H 7 I DNA-directed RNA polymerase II subunit RPB9 4932
36 3M3Y 7 I DNA-directed RNA polymerase II subunit RPB9 4932
37 4A3I 9 I DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB9 4932
38 6BM4 7 I DNA-directed RNA polymerase II subunit RPB9 4932
39 4BY1 9 I DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB9 4932
40 4A3M 9 I DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB9 4932
41 6BLP 7 I DNA-directed RNA polymerase II subunit RPB9 4932
42 4Y7N 7 I DNA-directed RNA polymerase II subunit RPB9 4932
43 5IP9 9 I DNA-directed RNA polymerase II subunit RPB9 4932
44 1I3Q 7 I DNA-DIRECTED RNA POLYMERASE II 14.2KD POLYPEPTIDE 4932 2.7.7.6 | Details
45 4BBS 9 I DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB9 4932
46 6BLO 7 I DNA-directed RNA polymerase II subunit RPB9 4932
47 1TWC 7 I DNA-DIRECTED RNA POLYMERASE II 14.2KD POLYPEPTIDE 4932 2.7.7.6 | Details
48 4Y52 7 I DNA-directed RNA polymerase II subunit RPB9 4932
49 6BQF 7 I DNA-directed RNA polymerase II subunit RPB9 4932
50 3HOU 9 I, U DNA-directed RNA polymerase II subunit RPB9 4932 2.7.7.6 | Details
51 3HOY 9 I DNA-directed RNA polymerase II subunit RPB9 4932 2.7.7.6 | Details
52 3HOV 9 I DNA-directed RNA polymerase II subunit RPB9 4932 2.7.7.6 | Details
53 6BM2 7 I DNA-directed RNA polymerase II subunit RPB9 4932
54 1TWA 7 I DNA-directed RNA polymerase II 14.2 kDa polypeptide 4932 2.7.7.6 | Details
55 5C3E 9 I DNA-directed RNA polymerase II subunit RPB9 4932
56 5W51 7 I DNA-directed RNA polymerase II subunit RPB9 4932
57 2NVT 10 I DNA-directed RNA polymerase II subunit 9 4932 2.7.7.6 | Details
58 3HOZ 9 I DNA-directed RNA polymerase II subunit RPB9 4932 2.7.7.6 | Details
59 3HOW 9 I DNA-directed RNA polymerase II subunit RPB9 4932 2.7.7.6 | Details
60 3HOX 9 I DNA-directed RNA polymerase II subunit RPB9 4932 2.7.7.6 | Details
61 1I6H 9 I DNA-DIRECTED RNA POLYMERASE II 14.2KD POLYPEPTIDE 4932 2.7.7.6 | Details
62 2R92 11 I DNA-directed RNA polymerase II subunit RPB9 4932 2.7.7.6 | Details
63 5W4U 7 I DNA-directed RNA polymerase II subunit RPB9 4932
64 2R7Z 12 I DNA-directed RNA polymerase II subunit RPB9 4932 2.7.7.6 | Details
65 1R9T 10 I DNA-directed RNA polymerase II 14.2 kDa polypeptide 4932 2.7.7.6 | Details
66 3I4M 9 I DNA-directed RNA polymerase II subunit RPB9 4932
67 3H3V 9 J DNA-directed RNA polymerase II subunit RPB9 4932 2.7.7.6 | Details
68 5U5Q 9 I DNA-directed RNA polymerase II subunit RPB9 4932
69 1TWH 7 I DNA-directed RNA polymerase II 14.2 kDa polypeptide 4932 2.7.7.6 | Details
70 2NVY 7 I DNA-directed RNA polymerase II subunit 9 4932 2.7.7.6 | Details
71 2E2J 10 I DNA-directed RNA polymerase II subunit 9 4932 2.7.7.6 | Details
72 5C4X 9 I DNA-directed RNA polymerase II subunit RPB9 4932
73 2VUM 9 I DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB9 4932 2.7.7.6 | Details
74 5C44 9 I DNA-directed RNA polymerase II subunit RPB9 4932
75 3M4O 7 I DNA-directed RNA polymerase II subunit RPB9 4932
76 5C4J 7 I DNA-directed RNA polymerase II subunit RPB9 4932
77 2R93 10 I DNA-directed RNA polymerase II subunit RPB9 4932 2.7.7.6 | Details
78 1TWG 7 I DNA-directed RNA polymerase II 14.2 kDa polypeptide 4932 2.7.7.6 | Details
79 3GTM 7 I DNA-directed RNA polymerase II subunit RPB9 DNA-directed RNA polymerase II subunit 9 4932
80 3I4N 9 I DNA-directed RNA polymerase II subunit RPB9 4932
81 2E2I 10 I DNA-directed RNA polymerase II subunit 9 4932 2.7.7.6 | Details
82 3GTL 7 I DNA-directed RNA polymerase II subunit RPB9 DNA-directed RNA polymerase II subunit 9 4932
83 4BXZ 9 I DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB9 4932 2.7.7.6 | Details
84 3GTK 7 I DNA-directed RNA polymerase II subunit RPB9 DNA-directed RNA polymerase II subunit 9 4932
85 5C4A 9 I DNA-directed RNA polymerase II subunit RPB9 4932
86 3K1F 9 I DNA-directed RNA polymerase II subunit RPB9 4932 2.7.7.6 | Details
87 3GTJ 7 I DNA-directed RNA polymerase II subunit RPB9 DNA-directed RNA polymerase II subunit 9 4932
88 3GTG 7 I DNA-directed RNA polymerase II subunit RPB9 DNA-directed RNA polymerase II subunit 9 4932
89 2YU9 10 I DNA-directed RNA polymerase II subunit 9 4932 2.7.7.6 | Details
90 1WCM 9 I DNA-DIRECTED RNA POLYMERASE II 14.2 KDA POLYPEPTIDE 4932 2.7.7.6 | Details
91 2JA7 12 I, U DNA-DIRECTED RNA POLYMERASE II SUBUNIT 9 4932 2.7.7.6 | Details
92 4X6A 7 I DNA-directed RNA polymerase II subunit RPB9 4932
93 4X67 7 I DNA-directed RNA polymerase II subunit RPB9 4932
94 1Y1W 12 I DNA-directed RNA polymerase II subunit 9 4932 2.7.7.6 | Details
95 3K7A 7 I DNA-directed RNA polymerase II subunit RPB9 4932
96 5X50 9 I DNA-directed RNA polymerase subunit 460519
97 2JA8 9 I DNA-DIRECTED RNA POLYMERASE II SUBUNIT 9 4932 2.7.7.6 | Details
98 2JA5 9 I DNA-directed RNA polymerase II subunit RPB9 4932
99 2NVX 10 I DNA-directed RNA polymerase II subunit 9 4932 2.7.7.6 | Details
100 2B63 10 I DNA-directed RNA polymerase II subunit 9 4932 2.7.7.6 | Details
101 3GTQ 7 I DNA-directed RNA polymerase II subunit RPB9 DNA-directed RNA polymerase II subunit 9 4932
102 3GTP 7 I DNA-directed RNA polymerase II subunit RPB9 DNA-directed RNA polymerase II subunit 9 4932
103 1Y1V 9 I DNA-directed RNA polymerase II subunit 9 4932 2.7.7.6 | Details
104 3GTO 7 I DNA-directed RNA polymerase II subunit RPB9 DNA-directed RNA polymerase II subunit 9 4932
105 3H0G 9 I, U DNA-directed RNA polymerase II subunit RPB9 4896 1.1.1.357 | Details
106 3FKI 9 I DNA-directed RNA polymerase II subunit RPB9 4932
107 1Y1Y 11 I DNA-directed RNA polymerase II subunit 9 4932 2.7.7.6 | Details
108 1SFO 9 I DNA-directed RNA polymerase II 14.2 kDa polypeptide 4932 2.7.7.6 | Details
109 2E2H 10 I DNA-directed RNA polymerase II subunit 9 4932 2.7.7.6 | Details
110 2JA6 9 I DNA-DIRECTED RNA POLYMERASE II SUBUNIT 9 4932 2.7.7.6 | Details
111 2NVZ 10 I DNA-directed RNA polymerase II subunit 9 4932 2.7.7.6 | Details
112 1Y77 12 I DNA-directed RNA polymerase II subunit 9 4932 2.7.7.6 | Details
113 1NIK 9 I DNA-directed RNA polymerase II, chain RPB9 4932 2.7.7.6 | Details
114 1R9S 9 I DNA-directed RNA polymerase II 14.2 kDa polypeptide 4932 2.7.7.6 | Details
115 1R5U 7 I DNA-directed RNA polymerase II 14.2 kDa polypeptide 4932 2.7.7.6 | Details
116 2B8K 9 I DNA-directed RNA polymerase II subunit 9 4932 2.7.7.6 | Details
117 5X51 9 I, U DNA-directed RNA polymerase subunit 460519
118 5X4Z 9 I, U DNA-directed RNA polymerase subunit 460519
119 5OQM 9 I DNA-directed RNA polymerase II subunit RPB9 4932
120 5OQJ 9 I DNA-directed RNA polymerase II subunit RPB9 4932
121 5XON 9 I DNA-directed RNA polymerase subunit 460519
122 5VVS 9 I DNA-directed RNA polymerase II subunit RPB9 4932
123 5VVR 9 I DNA-directed RNA polymerase II subunit RPB9 4932
124 5U0S 25 i RNA polymerase II subunit Rpb9 4896 1.1.1.357 | Details
125 5SVA 9 I DNA-directed RNA polymerase II subunit RPB9 4932
126 5FYW 9 I DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB9 4932
127 5FZ5 9 I DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB9 4932
128 5FMF 11 I DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB9 4932
129 4V1M 7 I DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB9 4932
130 4V1N 9 I DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB9 4932
131 4V1O 9 I DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB9 4932
132 3J1N 9 I DNA-directed RNA polymerase II subunit RPB9 4932
133 3J0K 9 I DNA-directed RNA polymerase II subunit 9 9606 2.7.7.6 | Details
134 1PQV 9 I DNA-directed RNA polymerase II 14.2 kDa polypeptide 4932 2.7.7.6 | Details
135 1NT9 9 I DNA-directed RNA polymerase II 14.2 kDa polypeptide 4932 2.7.7.6 | Details