Sequence Similarity Clusters for the Entities in PDB 1NT9

Entity #1 | 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 % 125 125 241
95 % 125 125 319 Flexibility: Low
Max RMSD: 5.3, Avg RMSD: 1.6
PDBFlex
90 % 125 125 328
70 % 130 130 352
50 % 143 143 376
40 % 143 143 407
30 % 143 143 408
Entity #10 | Chains: J
DNA-directed RNA polymerases I, II, and III 8.3 kDa polypeptide protein, length: 70 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name Structural variation in cluster
100 % 160 160 183
95 % 160 160 234 Flexibility: No
Max RMSD: 1.1, Avg RMSD: 0.5
PDBFlex
90 % 160 160 241
70 % 178 178 234
50 % 186 186 230
40 % 186 186 256
30 % 186 186 276
Entity #11 | Chains: K
DNA-DIRECTED RNA POLYMERASE II 13.6 KD POLYPEPTIDE protein, length: 120 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name Structural variation in cluster
100 % 127 127 231
95 % 127 127 308 Flexibility: No
Max RMSD: 1.0, Avg RMSD: 0.5
PDBFlex
90 % 127 127 318
70 % 127 127 369
50 % 132 132 411
40 % 134 134 427
30 % 134 134 437
Entity #12 | 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 % 156 156 187
95 % 156 156 240 Flexibility: Low
Max RMSD: 2.0, Avg RMSD: 1.0
PDBFlex
90 % 156 156 249
70 % 156 156 280
50 % 161 161 294
40 % 161 161 322
30 % 161 161 330
Entity #2 | Chains: B
DNA-directed polymerase II SECOND LARGEST SUBUNIT protein, length: 1224 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name Structural variation in cluster
100 % 127 127 233
95 % 127 127 309 Flexibility: Low
Max RMSD: 3.3, Avg RMSD: 1.3
PDBFlex
90 % 127 127 319
70 % 134 134 334
50 % 145 145 371
40 % 153 153 350
30 % 304 306 144
Entity #3 | 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 % 122 122 246
95 % 122 122 326 Flexibility: Low
Max RMSD: 1.0, Avg RMSD: 0.5
PDBFlex
90 % 122 122 339
70 % 122 122 382
50 % 122 122 450
40 % 122 122 479
30 % 122 122 484
Entity #4 | Chains: D
YEAST DNA-DIRECTED RNA POLYMERASE II 32 KD POLYPEPTIDE protein, length: 221 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name Structural variation in cluster
100 % 66 66 598
95 % 66 66 734 Flexibility: Low
Max RMSD: 3.5, Avg RMSD: 0.7
PDBFlex
90 % 66 66 759
70 % 69 69 766
50 % 74 74 744
40 % 74 74 777
30 % 74 74 779
Entity #5 | 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 % 161 161 182
95 % 161 161 233 Flexibility: Low
Max RMSD: 2.1, Avg RMSD: 0.7
PDBFlex
90 % 161 161 239
70 % 166 166 254
50 % 168 168 271
40 % 179 179 281
30 % 179 179 295
Entity #6 | 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 % 155 155 188
95 % 155 155 241 Flexibility: Low
Max RMSD: 1.4, Avg RMSD: 0.6
PDBFlex
90 % 155 155 250
70 % 155 155 281
50 % 173 174 260
40 % 173 174 288
30 % 173 174 301
Entity #7 | Chains: G
DNA-DIRECTED RNA POLYMERASE II 19 KD POLYPEPTIDE protein, length: 171 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name Structural variation in cluster
100 % 69 69 537
95 % 69 69 673 Flexibility: Low
Max RMSD: 4.2, Avg RMSD: 0.7
PDBFlex
90 % 69 69 698
70 % 69 69 740
50 % 88 88 559
40 % 88 88 601
30 % 88 88 605
Entity #8 | Chains: H
DNA-DIRECTED RNA POLYMERASES I, II, AND III 14.5 KD POLYPEPTIDE protein, length: 146 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name Structural variation in cluster
100 % 159 160 184
95 % 160 161 232 Flexibility: Low
Max RMSD: 1.9, Avg RMSD: 1.0
PDBFlex
90 % 160 161 240
70 % 160 161 270
50 % 165 166 280
40 % 165 166 312
30 % 179 180 292
Entity #9 | Chains: I
DNA-directed RNA polymerase II 14.2 kDa polypeptide protein, length: 122 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name Structural variation in cluster
100 % 126 126 236
95 % 126 126 313 Flexibility: Low
Max RMSD: 2.9, Avg RMSD: 1.0
PDBFlex
90 % 126 126 323
70 % 131 131 348
50 % 133 133 401
40 % 133 133 432
30 % 144 144 405

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 1Y14 2 B, D DNA-directed RNA polymerase II 19 kDa polypeptide 4932 2.7.7.6 | Details
2 3PO2 7 G DNA-directed RNA polymerase II subunit RPB7 4932 2.7.7.6 | Details
3 3PO3 7 G DNA-directed RNA polymerase II subunit RPB7 4932 2.7.7.6 | Details
4 2C35 2 B, D, F, H DNA-DIRECTED RNA POLYMERASE II 19 KDA POLYPEPTIDE 9606
5 5XOG 7 G RNA polymerase II subunit 460519
6 4A3E 7 G RPB7, DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB7 4932
7 5OT2 7 G DNA-directed RNA polymerase II subunit RPB7 4932
8 4A3D 7 G RPB7, DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB7 4932
9 5IP7 7 G DNA-directed RNA polymerase II subunit RPB7 4932
10 4A3F 7 G RPB7, DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB7 4932
11 4A93 7 G RPB7, DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB7 4932
12 4BY7 7 G DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB7 4932
13 4A3C 7 G RPB7, DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB7 4932
14 4A3K 7 G RPB7, DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB7 4932
15 4A3L 7 G DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB7 4932
16 4BXX 7 G DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB7 4932
17 4A3G 7 G RPB7, DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB7 4932
18 4A3B 7 G RPB7, DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB7 4932
19 4BBR 7 G DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB7 4932
20 4A3J 7 G RPB7, DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB7 4932
21 4A3I 7 G RPB7, DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB7 4932
22 4BY1 7 G DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB7 4932
23 4A3M 7 G DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB7 4932
24 5IP9 7 G DNA-directed RNA polymerase II subunit RPB7 4932
25 4BBS 7 G DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB7 4932
26 3HOU 7 G, S DNA-directed RNA polymerase II subunit RPB7 4932 2.7.7.6 | Details
27 3HOY 7 G DNA-directed RNA polymerase II subunit RPB7 4932 2.7.7.6 | Details
28 3HOV 7 G DNA-directed RNA polymerase II subunit RPB7 4932 2.7.7.6 | Details
29 5C3E 7 G DNA-directed RNA polymerase II subunit RPB7 4932
30 3HOZ 7 G DNA-directed RNA polymerase II subunit RPB7 4932 2.7.7.6 | Details
31 3HOW 7 G DNA-directed RNA polymerase II subunit RPB7 4932 2.7.7.6 | Details
32 3HOX 7 G DNA-directed RNA polymerase II subunit RPB7 4932 2.7.7.6 | Details
33 2R92 9 G DNA-directed RNA polymerase II subunit RPB7 4932 2.7.7.6 | Details
34 2R7Z 10 G DNA-directed RNA polymerase II subunit RPB7 4932 2.7.7.6 | Details
35 3I4M 7 G DNA-directed RNA polymerase II subunit RPB7 4932
36 3H3V 7 H DNA-directed RNA polymerase II subunit RPB7 4932 2.7.7.6 | Details
37 5U5Q 7 G DNA-directed RNA polymerase II subunit RPB7 4932
38 5C4X 7 G DNA-directed RNA polymerase II subunit RPB7 4932
39 2VUM 7 G DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB7 4932 2.7.7.6 | Details
40 5C44 7 G DNA-directed RNA polymerase II subunit RPB7 4932
41 2R93 8 G DNA-directed RNA polymerase II subunit RPB7 4932 2.7.7.6 | Details
42 3I4N 7 G DNA-directed RNA polymerase II subunit RPB7 4932
43 4BXZ 7 G DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB7 4932 2.7.7.6 | Details
44 5C4A 7 G DNA-directed RNA polymerase II subunit RPB7 4932
45 3K1F 7 G DNA-directed RNA polymerase II subunit RPB7 4932 2.7.7.6 | Details
46 1WCM 7 G DNA-DIRECTED RNA POLYMERASE II 19 KD POLYPEPTIDE 4932 2.7.7.6 | Details
47 2JA7 10 G, S DNA-DIRECTED RNA POLYMERASE II 19KDA POLYPEPTIDE 4932 2.7.7.6 | Details
48 1Y1W 10 G DNA-directed RNA polymerase II 19 kDa polypeptide 4932 2.7.7.6 | Details
49 3QT1 7 G DNA-directed RNA polymerase II subunit RPB7 4932 2.7.7.6 | Details
50 5X50 7 G RNA polymerase II subunit 460519
51 2JA8 7 G DNA-DIRECTED RNA POLYMERASE II 19KDA POLYPEPTIDE 4932 2.7.7.6 | Details
52 2JA5 7 G DNA-directed RNA polymerase II subunit RPB7 4932
53 2B63 8 G DNA-directed RNA polymerase II 19 kDa polypeptide 4932 2.7.7.6 | Details
54 1Y1V 7 G DNA-directed RNA polymerase II 19 kDa polypeptide 4932 2.7.7.6 | Details
55 3H0G 7 G, S DNA-directed RNA polymerase II subunit rpb7 4896
56 3FKI 7 G DNA-directed RNA polymerase II subunit RPB7 4932
57 1Y1Y 9 G DNA-directed RNA polymerase II 19 kDa polypeptide 4932 2.7.7.6 | Details
58 2JA6 7 G DNA-DIRECTED RNA POLYMERASE II 19KDA POLYPEPTIDE 4932 2.7.7.6 | Details
59 1Y77 10 G DNA-directed RNA polymerase II 19 kDa polypeptide 4932 2.7.7.6 | Details
60 5X51 7 G, S RNA polymerase II subunit 460519
61 5X4Z 7 G, S RNA polymerase II subunit 460519
62 6EXV 7 G DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB7 9823
63 5OQM 7 G DNA-directed RNA polymerase II subunit RPB7 4932
64 5OQJ 7 G DNA-directed RNA polymerase II subunit RPB7 4932
65 5OIK 7 G DNA-directed RNA polymerase II subunit RPB7 9913
66 5XON 7 G RNA polymerase II subunit 460519
67 5VVS 7 G DNA-directed RNA polymerase II subunit RPB7 4932
68 5VVR 7 G DNA-directed RNA polymerase II subunit RPB7 4932
69 5U0S 23 g RNA polymerase II subunit Rpb7 4896
70 5SVA 7 G DNA-directed RNA polymerase II subunit RPB7 4932
71 5IY6 7 G DNA-directed RNA polymerase II subunit RPB7 9606
72 5IY7 7 G DNA-directed RNA polymerase II subunit RPB7 9606
73 5IY8 7 G DNA-directed RNA polymerase II subunit RPB7 9606
74 5IY9 7 G DNA-directed RNA polymerase II subunit RPB7 9606
75 5IYA 7 G DNA-directed RNA polymerase II subunit RPB7 9606
76 5IYB 7 G DNA-directed RNA polymerase II subunit RPB7 9606
77 5IYC 7 G DNA-directed RNA polymerase II subunit RPB7 9606
78 5IYD 7 G DNA-directed RNA polymerase II subunit RPB7 9606
79 5FYW 7 G DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB7 4932
80 5FZ5 7 G DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB7 4932
81 5FMF 9 G DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB7 4932
82 5FLM 7 G DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB7 9913
83 4V1N 7 G DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB7 4932
84 4V1O 7 G DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB7 4932
85 3J1N 7 G DNA-directed RNA polymerase II subunit RPB7 4932
86 3J0K 7 G DNA-directed RNA polymerase II 19 kDa polypeptide 9606 2.7.7.6 | Details
87 1PQV 7 G DNA-directed RNA polymerase II 19 kDa polypeptide 4932 2.7.7.6 | Details
88 1NT9 7 G DNA-DIRECTED RNA POLYMERASE II 19 KD POLYPEPTIDE 4932 2.7.7.6 | Details