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 % 127 127 248
95 % 127 127 322 Flexibility: Low
Max RMSD: 6.8, Avg RMSD: 1.6
PDBFlex
90 % 127 127 334
70 % 139 139 345
50 % 154 154 373
40 % 154 154 406
30 % 154 154 406
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 % 168 168 185
95 % 168 168 237 Flexibility: No
Max RMSD: 1.1, Avg RMSD: 0.5
PDBFlex
90 % 168 168 244
70 % 195 195 216
50 % 203 203 225
40 % 203 203 251
30 % 203 203 264
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 % 129 129 242
95 % 129 129 309 Flexibility: No
Max RMSD: 1.1, Avg RMSD: 0.5
PDBFlex
90 % 129 129 320
70 % 129 129 373
50 % 141 141 407
40 % 143 143 426
30 % 143 143 421
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 % 164 164 187
95 % 164 164 239 Flexibility: Low
Max RMSD: 2.0, Avg RMSD: 1.0
PDBFlex
90 % 164 164 248
70 % 164 164 277
50 % 176 176 279
40 % 176 176 309
30 % 176 176 319
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 % 129 129 244
95 % 129 129 315 Flexibility: Low
Max RMSD: 3.3, Avg RMSD: 1.2
PDBFlex
90 % 129 129 325
70 % 143 143 332
50 % 156 156 359
40 % 164 164 349
30 % 330 332 142
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 % 124 124 256
95 % 124 124 331 Flexibility: Low
Max RMSD: 1.0, Avg RMSD: 0.5
PDBFlex
90 % 124 124 345
70 % 124 124 389
50 % 124 124 456
40 % 124 124 493
30 % 124 124 496
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 66 636
95 % 66 66 778 Flexibility: Low
Max RMSD: 3.5, Avg RMSD: 0.8
PDBFlex
90 % 66 66 806
70 % 69 69 808
50 % 81 81 692
40 % 81 81 727
30 % 81 81 740
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 % 169 169 184
95 % 169 169 234 Flexibility: Low
Max RMSD: 2.1, Avg RMSD: 0.7
PDBFlex
90 % 169 169 241
70 % 181 181 241
50 % 183 183 260
40 % 196 196 270
30 % 196 196 286
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 % 163 163 189
95 % 163 163 241 Flexibility: Low
Max RMSD: 1.4, Avg RMSD: 0.6
PDBFlex
90 % 163 163 250
70 % 163 163 282
50 % 190 191 246
40 % 190 191 278
30 % 190 191 291
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 69 565
95 % 69 69 703 Flexibility: Low
Max RMSD: 4.4, Avg RMSD: 0.7
PDBFlex
90 % 69 69 732
70 % 69 69 776
50 % 97 97 533
40 % 97 97 576
30 % 97 97 581
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 % 167 168 186
95 % 168 169 235 Flexibility: Low
Max RMSD: 1.9, Avg RMSD: 0.9
PDBFlex
90 % 168 169 242
70 % 168 169 271
50 % 180 181 267
40 % 180 181 299
30 % 196 197 282
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 % 128 128 245
95 % 128 128 316 Flexibility: Low
Max RMSD: 2.9, Avg RMSD: 1.0
PDBFlex
90 % 128 128 326
70 % 140 140 341
50 % 142 142 404
40 % 142 142 431
30 % 157 157 397

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


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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 6A5O 7 G RNA polymerase II subunit 460519
63 6A5P 7 G RNA polymerase II subunit 460519
64 6A5R 7 G RNA polymerase II subunit 460519
65 6A5T 7 G RNA polymerase II subunit 460519
66 6A5U 7 G RNA polymerase II subunit 460519
67 6A5V 7 G RNA polymerase II subunit 460519
68 6A5L 7 G RNA polymerase II subunit 460519
69 6GML 21 G RNA polymerase II subunit G 9823
70 6GMH 7 G RNA polymerase II subunit G 9823
71 6EXV 7 G DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB7 9823
72 5OQM 7 G DNA-directed RNA polymerase II subunit RPB7 4932
73 5OQJ 7 G DNA-directed RNA polymerase II subunit RPB7 4932
74 5OIK 7 G DNA-directed RNA polymerase II subunit RPB7 9913
75 5XON 7 G RNA polymerase II subunit 460519
76 5VVS 7 G DNA-directed RNA polymerase II subunit RPB7 4932
77 5VVR 7 G DNA-directed RNA polymerase II subunit RPB7 4932
78 5U0S 23 g RNA polymerase II subunit Rpb7 4896
79 5SVA 7 G DNA-directed RNA polymerase II subunit RPB7 4932
80 5IY6 7 G DNA-directed RNA polymerase II subunit RPB7 9606
81 5IY7 7 G DNA-directed RNA polymerase II subunit RPB7 9606
82 5IY8 7 G DNA-directed RNA polymerase II subunit RPB7 9606
83 5IY9 7 G DNA-directed RNA polymerase II subunit RPB7 9606
84 5IYA 7 G DNA-directed RNA polymerase II subunit RPB7 9606
85 5IYB 7 G DNA-directed RNA polymerase II subunit RPB7 9606
86 5IYC 7 G DNA-directed RNA polymerase II subunit RPB7 9606
87 5IYD 7 G DNA-directed RNA polymerase II subunit RPB7 9606
88 5FYW 7 G DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB7 4932
89 5FZ5 7 G DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB7 4932
90 5FMF 9 G DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB7 4932
91 5FLM 7 G DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB7 9913
92 4V1N 7 G DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB7 4932
93 4V1O 7 G DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB7 4932
94 3J1N 7 G DNA-directed RNA polymerase II subunit RPB7 4932
95 3J0K 7 G DNA-directed RNA polymerase II 19 kDa polypeptide 9606 2.7.7.6 | Details
96 1PQV 7 G DNA-directed RNA polymerase II 19 kDa polypeptide 4932 2.7.7.6 | Details
97 1NT9 7 G DNA-DIRECTED RNA POLYMERASE II 19 KD POLYPEPTIDE 4932 2.7.7.6 | Details