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 % 127 127 241
95 % 127 127 316 Flexibility: Low
Max RMSD: 6.8, Avg RMSD: 1.6
PDBFlex
90 % 127 127 328
70 % 132 132 352
50 % 145 145 391
40 % 145 145 414
30 % 145 145 410
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 % 162 162 186
95 % 162 162 238 Flexibility: No
Max RMSD: 1.1, Avg RMSD: 0.5
PDBFlex
90 % 162 162 248
70 % 180 180 236
50 % 188 188 237
40 % 188 188 262
30 % 188 188 278
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 % 129 129 236
95 % 129 129 305 Flexibility: No
Max RMSD: 1.1, Avg RMSD: 0.5
PDBFlex
90 % 129 129 317
70 % 129 129 368
50 % 134 134 418
40 % 136 136 433
30 % 136 136 433
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 % 158 158 188
95 % 158 158 244 Flexibility: Low
Max RMSD: 2.0, Avg RMSD: 1.0
PDBFlex
90 % 158 158 253
70 % 158 158 284
50 % 163 163 305
40 % 163 163 338
30 % 163 163 343
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 % 129 129 237
95 % 129 129 310 Flexibility: Low
Max RMSD: 3.3, Avg RMSD: 1.2
PDBFlex
90 % 129 129 321
70 % 136 136 341
50 % 147 147 383
40 % 155 155 365
30 % 316 318 139
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 % 124 124 250
95 % 124 124 326 Flexibility: Low
Max RMSD: 1.0, Avg RMSD: 0.5
PDBFlex
90 % 124 124 337
70 % 124 124 382
50 % 124 124 450
40 % 124 124 483
30 % 124 124 488
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 66 619
95 % 66 66 757 Flexibility: Low
Max RMSD: 3.5, Avg RMSD: 0.8
PDBFlex
90 % 66 66 785
70 % 69 69 794
50 % 74 74 761
40 % 74 74 790
30 % 74 74 796
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 % 163 163 185
95 % 163 163 236 Flexibility: Low
Max RMSD: 2.1, Avg RMSD: 0.7
PDBFlex
90 % 163 163 245
70 % 168 168 261
50 % 170 170 282
40 % 181 181 283
30 % 181 181 298
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 % 157 157 189
95 % 157 157 245 Flexibility: Low
Max RMSD: 1.4, Avg RMSD: 0.6
PDBFlex
90 % 157 157 254
70 % 157 157 287
50 % 175 176 267
40 % 175 176 295
30 % 175 176 305
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 69 555
95 % 69 69 690 Flexibility: Low
Max RMSD: 4.4, Avg RMSD: 0.7
PDBFlex
90 % 69 69 717
70 % 69 69 762
50 % 88 88 572
40 % 88 88 614
30 % 88 88 614
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 % 161 162 187
95 % 162 163 237 Flexibility: Low
Max RMSD: 1.9, Avg RMSD: 0.9
PDBFlex
90 % 162 163 247
70 % 162 163 278
50 % 167 168 292
40 % 167 168 325
30 % 181 182 292
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 % 128 128 239
95 % 128 128 311 Flexibility: Low
Max RMSD: 2.9, Avg RMSD: 1.0
PDBFlex
90 % 128 128 322
70 % 133 133 348
50 % 135 135 415
40 % 135 135 438
30 % 146 146 409

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