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 % 110 173 271
50 % 112 192 263
40 % 112 192 292
30 % 113 208 277
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 % 104 132 242
95 % 104 132 309 Flexibility: Low
Max RMSD: 2.9, Avg RMSD: 1.0
PDBFlex
90 % 104 132 321
70 % 106 151 331
50 % 107 153 389
40 % 107 153 416
30 % 107 168 388
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 % 113 206 192
50 % 118 214 220
40 % 118 214 248
30 % 118 214 263
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 % 105 133 240
95 % 105 133 306 Flexibility: No
Max RMSD: 1.1, Avg RMSD: 0.5
PDBFlex
90 % 105 133 318
70 % 105 133 367
50 % 107 152 399
40 % 108 154 415
30 % 108 154 417
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 % 108 168 283
50 % 110 187 269
40 % 110 187 304
30 % 110 187 316
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 29124
95 % 4 5 15929 Flexibility: Low
Max RMSD: 2.8, Avg RMSD: 1.9
PDBFlex
90 % 4 5 16481
70 % 4 5 15311
50 % 4 6 11072
40 % 4 6 9977
30 % 4 6 8527
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 % 105 131 248
95 % 105 131 317 Flexibility: Low
Max RMSD: 6.8, Avg RMSD: 1.6
PDBFlex
90 % 105 131 328
70 % 107 150 334
50 % 108 165 352
40 % 108 165 393
30 % 108 165 394
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 % 105 133 241
95 % 105 133 307 Flexibility: Low
Max RMSD: 3.3, Avg RMSD: 1.2
PDBFlex
90 % 105 133 319
70 % 108 154 319
50 % 108 167 349
40 % 113 175 337
30 % 224 359 139
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 % 103 128 252
95 % 103 128 326 Flexibility: Low
Max RMSD: 1.0, Avg RMSD: 0.5
PDBFlex
90 % 103 128 337
70 % 103 128 384
50 % 103 128 458
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 70 598
95 % 51 70 736 Flexibility: Low
Max RMSD: 3.5, Avg RMSD: 0.8
PDBFlex
90 % 51 70 770
70 % 52 73 777
50 % 54 92 626
40 % 54 92 659
30 % 54 92 662
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 % 113 192 232
50 % 114 194 252
40 % 114 207 265
30 % 114 207 280
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 % 108 167 288
50 % 111 202 245
40 % 111 202 273
30 % 111 202 285
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 73 559
95 % 53 73 688 Flexibility: Low
Max RMSD: 4.4, Avg RMSD: 0.7
PDBFlex
90 % 53 73 711
70 % 53 73 763
50 % 57 108 493
40 % 57 108 545
30 % 57 108 542

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 3S1M 7 I DNA-directed RNA polymerase II subunit RPB9 4932
8 4A3E 9 I DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB9 4932
9 5OT2 9 I DNA-directed RNA polymerase II subunit RPB9 4932
10 3S1R 7 I DNA-directed RNA polymerase II subunit RPB9 4932
11 4A3D 9 I DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB9 4932
12 3S1N 7 I DNA-directed RNA polymerase II subunit RPB9 4932
13 5IP7 9 I DNA-directed RNA polymerase II subunit RPB9 4932
14 4A3F 9 I DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB9 4932
15 4A93 9 I DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB9 4932
16 1K83 7 I DNA-DIRECTED RNA POLYMERASE II 14.2KD POLYPEPTIDE 4932 2.7.7.6 | Details
17 1I50 7 I DNA-DIRECTED RNA POLYMERASE II 14.2KD POLYPEPTIDE 4932 2.7.7.6 | Details
18 4BY7 9 I DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB9 4932
19 3S2D 7 I DNA-directed RNA polymerase II subunit RPB9 4932
20 4A3C 9 I DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB9 4932
21 4A3K 9 I DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB9 4932
22 3S15 7 I DNA-directed RNA polymerase II subunit RPB9 4932
23 4A3L 9 I DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB9 4932
24 4BXX 9 I DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB9 4932
25 3S1Q 7 I DNA-directed RNA polymerase II subunit RPB9 4932
26 3S16 7 I DNA-directed RNA polymerase II subunit RPB9 4932
27 3S17 7 I DNA-directed RNA polymerase II subunit RPB9 4932
28 4A3G 9 I DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB9 4932
29 4A3B 9 I DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB9 4932
30 4BBR 9 I DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB9 4932
31 2NVQ 10 I DNA-directed RNA polymerase II subunit 9 4932 2.7.7.6 | Details
32 3RZD 7 I DNA-directed RNA polymerase II subunit RPB9 4932
33 4A3J 9 I DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB9 4932
34 3S2H 7 I DNA-directed RNA polymerase II subunit RPB9 4932
35 3M3Y 7 I DNA-directed RNA polymerase II subunit RPB9 4932
36 4A3I 9 I DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB9 4932
37 6BM4 7 I DNA-directed RNA polymerase II subunit RPB9 4932
38 4BY1 9 I DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB9 4932
39 4A3M 9 I DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB9 4932
40 6BLP 7 I DNA-directed RNA polymerase II subunit RPB9 4932
41 4Y7N 7 I DNA-directed RNA polymerase II subunit RPB9 4932
42 5IP9 9 I DNA-directed RNA polymerase II subunit RPB9 4932
43 1I3Q 7 I DNA-DIRECTED RNA POLYMERASE II 14.2KD POLYPEPTIDE 4932 2.7.7.6 | Details
44 4BBS 9 I DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB9 4932
45 6BLO 7 I DNA-directed RNA polymerase II subunit RPB9 4932
46 1TWC 7 I DNA-DIRECTED RNA POLYMERASE II 14.2KD POLYPEPTIDE 4932 2.7.7.6 | Details
47 4Y52 7 I DNA-directed RNA polymerase II subunit RPB9 4932
48 6BQF 7 I DNA-directed RNA polymerase II subunit RPB9 4932
49 3HOU 9 I, U DNA-directed RNA polymerase II subunit RPB9 4932 2.7.7.6 | Details
50 3HOY 9 I DNA-directed RNA polymerase II subunit RPB9 4932 2.7.7.6 | Details
51 3HOV 9 I DNA-directed RNA polymerase II subunit RPB9 4932 2.7.7.6 | Details
52 6BM2 7 I DNA-directed RNA polymerase II subunit RPB9 4932
53 1TWA 7 I DNA-directed RNA polymerase II 14.2 kDa polypeptide 4932 2.7.7.6 | Details
54 5C3E 9 I DNA-directed RNA polymerase II subunit RPB9 4932
55 5W51 7 I DNA-directed RNA polymerase II subunit RPB9 4932
56 2NVT 10 I DNA-directed RNA polymerase II subunit 9 4932 2.7.7.6 | Details
57 3HOZ 9 I DNA-directed RNA polymerase II subunit RPB9 4932 2.7.7.6 | Details
58 3HOW 9 I DNA-directed RNA polymerase II subunit RPB9 4932 2.7.7.6 | Details
59 3HOX 9 I DNA-directed RNA polymerase II subunit RPB9 4932 2.7.7.6 | Details
60 1I6H 9 I DNA-DIRECTED RNA POLYMERASE II 14.2KD POLYPEPTIDE 4932 2.7.7.6 | Details
61 2R92 11 I DNA-directed RNA polymerase II subunit RPB9 4932 2.7.7.6 | Details
62 5W4U 7 I DNA-directed RNA polymerase II subunit RPB9 4932
63 2R7Z 12 I DNA-directed RNA polymerase II subunit RPB9 4932 2.7.7.6 | Details
64 1R9T 10 I DNA-directed RNA polymerase II 14.2 kDa polypeptide 4932 2.7.7.6 | Details
65 3I4M 9 I DNA-directed RNA polymerase II subunit RPB9 4932
66 3H3V 9 J DNA-directed RNA polymerase II subunit RPB9 4932 2.7.7.6 | Details
67 5U5Q 9 I DNA-directed RNA polymerase II subunit RPB9 4932
68 1TWH 7 I DNA-directed RNA polymerase II 14.2 kDa polypeptide 4932 2.7.7.6 | Details
69 2NVY 7 I DNA-directed RNA polymerase II subunit 9 4932 2.7.7.6 | Details
70 2E2J 10 I DNA-directed RNA polymerase II subunit 9 4932 2.7.7.6 | Details
71 5C4X 9 I DNA-directed RNA polymerase II subunit RPB9 4932
72 2VUM 9 I DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB9 4932 2.7.7.6 | Details
73 5C44 9 I DNA-directed RNA polymerase II subunit RPB9 4932
74 3M4O 7 I DNA-directed RNA polymerase II subunit RPB9 4932
75 5C4J 7 I DNA-directed RNA polymerase II subunit RPB9 4932
76 2R93 10 I DNA-directed RNA polymerase II subunit RPB9 4932 2.7.7.6 | Details
77 1TWG 7 I DNA-directed RNA polymerase II 14.2 kDa polypeptide 4932 2.7.7.6 | Details
78 3GTM 7 I DNA-directed RNA polymerase II subunit RPB9 DNA-directed RNA polymerase II subunit 9 4932
79 3I4N 9 I DNA-directed RNA polymerase II subunit RPB9 4932
80 2E2I 10 I DNA-directed RNA polymerase II subunit 9 4932 2.7.7.6 | Details
81 3GTL 7 I DNA-directed RNA polymerase II subunit RPB9 DNA-directed RNA polymerase II subunit 9 4932
82 4BXZ 9 I DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB9 4932 2.7.7.6 | Details
83 3GTK 7 I DNA-directed RNA polymerase II subunit RPB9 DNA-directed RNA polymerase II subunit 9 4932
84 5C4A 9 I DNA-directed RNA polymerase II subunit RPB9 4932
85 3K1F 9 I DNA-directed RNA polymerase II subunit RPB9 4932 2.7.7.6 | Details
86 3GTJ 7 I DNA-directed RNA polymerase II subunit RPB9 DNA-directed RNA polymerase II subunit 9 4932
87 3GTG 7 I DNA-directed RNA polymerase II subunit RPB9 DNA-directed RNA polymerase II subunit 9 4932
88 2YU9 10 I DNA-directed RNA polymerase II subunit 9 4932 2.7.7.6 | Details
89 1WCM 9 I DNA-DIRECTED RNA POLYMERASE II 14.2 KDA POLYPEPTIDE 4932 2.7.7.6 | Details
90 2JA7 12 I, U DNA-DIRECTED RNA POLYMERASE II SUBUNIT 9 4932 2.7.7.6 | Details
91 4X6A 7 I DNA-directed RNA polymerase II subunit RPB9 4932
92 4X67 7 I DNA-directed RNA polymerase II subunit RPB9 4932
93 1Y1W 12 I DNA-directed RNA polymerase II subunit 9 4932 2.7.7.6 | Details
94 3K7A 7 I DNA-directed RNA polymerase II subunit RPB9 4932
95 2JA8 9 I DNA-DIRECTED RNA POLYMERASE II SUBUNIT 9 4932 2.7.7.6 | Details
96 2JA5 9 I DNA-directed RNA polymerase II subunit RPB9 4932
97 2NVX 10 I DNA-directed RNA polymerase II subunit 9 4932 2.7.7.6 | Details
98 2B63 10 I DNA-directed RNA polymerase II subunit 9 4932 2.7.7.6 | Details
99 3GTQ 7 I DNA-directed RNA polymerase II subunit RPB9 DNA-directed RNA polymerase II subunit 9 4932
100 3GTP 7 I DNA-directed RNA polymerase II subunit RPB9 DNA-directed RNA polymerase II subunit 9 4932
101 1Y1V 9 I DNA-directed RNA polymerase II subunit 9 4932 2.7.7.6 | Details
102 3GTO 7 I DNA-directed RNA polymerase II subunit RPB9 DNA-directed RNA polymerase II subunit 9 4932
103 3FKI 9 I DNA-directed RNA polymerase II subunit RPB9 4932
104 1Y1Y 11 I DNA-directed RNA polymerase II subunit 9 4932 2.7.7.6 | Details
105 1SFO 9 I DNA-directed RNA polymerase II 14.2 kDa polypeptide 4932 2.7.7.6 | Details
106 2E2H 10 I DNA-directed RNA polymerase II subunit 9 4932 2.7.7.6 | Details
107 2JA6 9 I DNA-DIRECTED RNA POLYMERASE II SUBUNIT 9 4932 2.7.7.6 | Details
108 2NVZ 10 I DNA-directed RNA polymerase II subunit 9 4932 2.7.7.6 | Details
109 1Y77 12 I DNA-directed RNA polymerase II subunit 9 4932 2.7.7.6 | Details
110 1NIK 9 I DNA-directed RNA polymerase II, chain RPB9 4932 2.7.7.6 | Details
111 1R9S 9 I DNA-directed RNA polymerase II 14.2 kDa polypeptide 4932 2.7.7.6 | Details
112 1R5U 7 I DNA-directed RNA polymerase II 14.2 kDa polypeptide 4932 2.7.7.6 | Details
113 2B8K 9 I DNA-directed RNA polymerase II subunit 9 4932 2.7.7.6 | Details
114 6I84 15 I DNA-directed RNA polymerase II subunit RPB9 4932
115 6GYK 9 I DNA-directed RNA polymerase II subunit RPB9 4932
116 6GYL 9 I DNA-directed RNA polymerase II subunit RPB9 4932
117 6GYM 17 I DNA-directed RNA polymerase II subunit RPB9 4932
118 5OQM 9 I DNA-directed RNA polymerase II subunit RPB9 4932
119 5OQJ 9 I DNA-directed RNA polymerase II subunit RPB9 4932
120 5VVS 9 I DNA-directed RNA polymerase II subunit RPB9 4932
121 5VVR 9 I DNA-directed RNA polymerase II subunit RPB9 4932
122 5SVA 9 I DNA-directed RNA polymerase II subunit RPB9 4932
123 5FYW 9 I DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB9 4932
124 5FZ5 9 I DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB9 4932
125 5FMF 11 I DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB9 4932
126 4V1M 7 I DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB9 4932
127 4V1N 9 I DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB9 4932
128 4V1O 9 I DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB9 4932
129 3J1N 9 I DNA-directed RNA polymerase II subunit RPB9 4932
130 3J0K 9 I DNA-directed RNA polymerase II subunit 9 9606 2.7.7.6 | Details
131 1PQV 9 I DNA-directed RNA polymerase II 14.2 kDa polypeptide 4932 2.7.7.6 | Details
132 1NT9 9 I DNA-directed RNA polymerase II 14.2 kDa polypeptide 4932 2.7.7.6 | Details