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 % 110 169 235 Flexibility: Low
Max RMSD: 1.9, Avg RMSD: 0.9
PDBFlex
90 % 110 169 242
70 % 110 169 271
50 % 112 181 267
40 % 112 181 299
30 % 113 197 282
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 % 104 128 245
95 % 104 128 316 Flexibility: Low
Max RMSD: 2.9, Avg RMSD: 1.0
PDBFlex
90 % 104 128 326
70 % 106 140 341
50 % 107 142 404
40 % 107 142 431
30 % 107 157 397
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 % 110 168 237 Flexibility: No
Max RMSD: 1.1, Avg RMSD: 0.5
PDBFlex
90 % 110 168 244
70 % 113 195 216
50 % 118 203 225
40 % 118 203 251
30 % 118 203 264
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 % 105 129 242
95 % 105 129 309 Flexibility: No
Max RMSD: 1.1, Avg RMSD: 0.5
PDBFlex
90 % 105 129 320
70 % 105 129 373
50 % 107 141 407
40 % 108 143 426
30 % 108 143 421
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 % 108 164 239 Flexibility: Low
Max RMSD: 2.0, Avg RMSD: 1.0
PDBFlex
90 % 108 164 248
70 % 108 164 277
50 % 110 176 279
40 % 110 176 309
30 % 110 176 319
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 28498
95 % 4 5 15571 Flexibility: Low
Max RMSD: 2.8, Avg RMSD: 1.9
PDBFlex
90 % 4 5 16139
70 % 4 5 15014
50 % 4 6 10848
40 % 4 6 9782
30 % 4 6 8372
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 % 105 127 248
95 % 105 127 322 Flexibility: Low
Max RMSD: 6.8, Avg RMSD: 1.6
PDBFlex
90 % 105 127 334
70 % 107 139 345
50 % 108 154 373
40 % 108 154 406
30 % 108 154 406
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 % 105 129 244
95 % 105 129 315 Flexibility: Low
Max RMSD: 3.3, Avg RMSD: 1.2
PDBFlex
90 % 105 129 325
70 % 108 143 332
50 % 108 156 359
40 % 113 164 349
30 % 216 332 142
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 % 103 124 256
95 % 103 124 331 Flexibility: Low
Max RMSD: 1.0, Avg RMSD: 0.5
PDBFlex
90 % 103 124 345
70 % 103 124 389
50 % 103 124 456
40 % 103 124 493
30 % 103 124 496
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 66 636
95 % 51 66 778 Flexibility: Low
Max RMSD: 3.5, Avg RMSD: 0.8
PDBFlex
90 % 51 66 806
70 % 52 69 808
50 % 54 81 692
40 % 54 81 727
30 % 54 81 740
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 % 111 169 234 Flexibility: Low
Max RMSD: 2.1, Avg RMSD: 0.7
PDBFlex
90 % 111 169 241
70 % 113 181 241
50 % 114 183 260
40 % 114 196 270
30 % 114 196 286
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 % 108 163 241 Flexibility: Low
Max RMSD: 1.4, Avg RMSD: 0.6
PDBFlex
90 % 108 163 250
70 % 108 163 282
50 % 111 191 246
40 % 111 191 278
30 % 111 191 291
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 69 565
95 % 53 69 703 Flexibility: Low
Max RMSD: 4.4, Avg RMSD: 0.7
PDBFlex
90 % 53 69 732
70 % 53 69 776
50 % 57 97 533
40 % 57 97 576
30 % 57 97 581

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 6A5O 9 I DNA-directed RNA polymerase subunit 460519
120 6A5P 9 I DNA-directed RNA polymerase subunit 460519
121 6A5R 9 I DNA-directed RNA polymerase subunit 460519
122 6A5T 9 I DNA-directed RNA polymerase subunit 460519
123 6A5U 9 I DNA-directed RNA polymerase subunit 460519
124 6A5V 9 I DNA-directed RNA polymerase subunit 460519
125 6A5L 9 I DNA-directed RNA polymerase subunit 460519
126 5OQM 9 I DNA-directed RNA polymerase II subunit RPB9 4932
127 5OQJ 9 I DNA-directed RNA polymerase II subunit RPB9 4932
128 5XON 9 I DNA-directed RNA polymerase subunit 460519
129 5VVS 9 I DNA-directed RNA polymerase II subunit RPB9 4932
130 5VVR 9 I DNA-directed RNA polymerase II subunit RPB9 4932
131 5U0S 25 i RNA polymerase II subunit Rpb9 4896 1.1.1.357 | Details
132 5SVA 9 I DNA-directed RNA polymerase II subunit RPB9 4932
133 5FYW 9 I DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB9 4932
134 5FZ5 9 I DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB9 4932
135 5FMF 11 I DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB9 4932
136 4V1M 7 I DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB9 4932
137 4V1N 9 I DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB9 4932
138 4V1O 9 I DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB9 4932
139 3J1N 9 I DNA-directed RNA polymerase II subunit RPB9 4932
140 3J0K 9 I DNA-directed RNA polymerase II subunit 9 9606 2.7.7.6 | Details
141 1PQV 9 I DNA-directed RNA polymerase II 14.2 kDa polypeptide 4932 2.7.7.6 | Details
142 1NT9 9 I DNA-directed RNA polymerase II 14.2 kDa polypeptide 4932 2.7.7.6 | Details