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 % 127 127 244
95 % 127 127 319 Flexibility: Low
Max RMSD: 6.8, Avg RMSD: 1.6
PDBFlex
90 % 127 127 331
70 % 139 139 344
50 % 154 154 368
40 % 154 154 395
30 % 154 154 403
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 % 203 203 249
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 % 129 129 238
95 % 129 129 306 Flexibility: No
Max RMSD: 1.1, Avg RMSD: 0.5
PDBFlex
90 % 129 129 318
70 % 129 129 369
50 % 141 141 402
40 % 143 143 422
30 % 143 143 419
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 % 164 164 274
50 % 176 176 275
40 % 176 176 303
30 % 176 176 315
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 % 129 129 241
95 % 129 129 313 Flexibility: Low
Max RMSD: 3.3, Avg RMSD: 1.2
PDBFlex
90 % 129 129 324
70 % 143 143 329
50 % 156 156 351
40 % 164 164 339
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 % 124 124 253
95 % 124 124 328 Flexibility: Low
Max RMSD: 1.0, Avg RMSD: 0.5
PDBFlex
90 % 124 124 341
70 % 124 124 384
50 % 124 124 453
40 % 124 124 489
30 % 124 124 491
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 66 630
95 % 66 66 772 Flexibility: Low
Max RMSD: 3.5, Avg RMSD: 0.8
PDBFlex
90 % 66 66 798
70 % 69 69 801
50 % 81 81 684
40 % 81 81 723
30 % 81 81 731
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 % 169 169 233 Flexibility: Low
Max RMSD: 2.1, Avg RMSD: 0.7
PDBFlex
90 % 169 169 241
70 % 181 181 241
50 % 183 183 258
40 % 196 196 267
30 % 196 196 285
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 % 163 163 278
50 % 190 191 244
40 % 190 191 274
30 % 190 191 290
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 69 557
95 % 69 69 698 Flexibility: Low
Max RMSD: 4.4, Avg RMSD: 0.7
PDBFlex
90 % 69 69 727
70 % 69 69 769
50 % 97 97 531
40 % 97 97 574
30 % 97 97 577
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 % 168 169 268
50 % 180 181 264
40 % 180 181 296
30 % 196 197 281
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 % 128 128 242
95 % 128 128 314 Flexibility: Low
Max RMSD: 2.9, Avg RMSD: 1.0
PDBFlex
90 % 128 128 325
70 % 140 140 340
50 % 142 142 398
40 % 142 142 427
30 % 157 157 382

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