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 % 139 139 345
50 % 154 154 373
40 % 154 154 404
30 % 154 154 405
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 % 203 203 250
30 % 203 203 263
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 % 129 129 371
50 % 141 141 406
40 % 143 143 426
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 % 164 164 277
50 % 176 176 277
40 % 176 176 306
30 % 176 176 316
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 % 143 143 331
50 % 156 156 358
40 % 164 164 347
30 % 330 332 141
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 % 124 124 386
50 % 124 124 455
40 % 124 124 491
30 % 124 124 493
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 66 773 Flexibility: Low
Max RMSD: 3.5, Avg RMSD: 0.8
PDBFlex
90 % 66 66 799
70 % 69 69 802
50 % 81 81 687
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 % 196 196 268
30 % 196 196 284
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 % 163 163 281
50 % 190 191 245
40 % 190 191 277
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 69 558
95 % 69 69 698 Flexibility: Low
Max RMSD: 4.4, Avg RMSD: 0.7
PDBFlex
90 % 69 69 727
70 % 69 69 771
50 % 97 97 532
40 % 97 97 575
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 % 168 169 270
50 % 180 181 265
40 % 180 181 298
30 % 196 197 280
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 % 140 140 341
50 % 142 142 403
40 % 142 142 431
30 % 157 157 393

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 3PO2 4 D DNA-directed RNA polymerase II subunit RPB4 4932 2.7.7.6 | Details
2 3PO3 4 D DNA-directed RNA polymerase II subunit RPB4 4932 2.7.7.6 | Details
3 4A3E 4 D DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB4 4932
4 5OT2 4 D DNA-directed RNA polymerase II subunit RPB4 4932
5 4A3D 4 D DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB4 4932
6 5IP7 4 D DNA-directed RNA polymerase II subunit RPB4 4932
7 4A3F 4 D DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB4 4932
8 4A93 4 D DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB4 4932
9 4BY7 4 D DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB4 4932
10 4A3C 4 D DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB4 4932
11 4A3K 4 D DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB4 4932
12 4A3L 4 D DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB4 4932
13 4BXX 4 D DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB4 4932
14 4A3G 4 D DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB4 4932
15 4A3B 4 D DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB4 4932
16 4BBR 4 D DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB4 4932
17 4A3J 4 D DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB4 4932
18 4A3I 4 D DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB4 4932
19 4BY1 4 D DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB4 4932
20 4A3M 4 D DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB4 4932
21 5IP9 4 D DNA-directed RNA polymerase II subunit RPB4 4932
22 4BBS 4 D DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB4 4932
23 3HOU 4 D, P DNA-directed RNA polymerase II subunit RPB4 4932 2.7.7.6 | Details
24 3HOY 4 D DNA-directed RNA polymerase II subunit RPB4 4932 2.7.7.6 | Details
25 3HOV 4 D DNA-directed RNA polymerase II subunit RPB4 4932 2.7.7.6 | Details
26 5C3E 4 D DNA-directed RNA polymerase II subunit RPB4 4932
27 3HOZ 4 D DNA-directed RNA polymerase II subunit RPB4 4932 2.7.7.6 | Details
28 3HOW 4 D DNA-directed RNA polymerase II subunit RPB4 4932 2.7.7.6 | Details
29 3HOX 4 D DNA-directed RNA polymerase II subunit RPB4 4932 2.7.7.6 | Details
30 2R92 6 D DNA-directed RNA polymerase II subunit RPB4 4932 2.7.7.6 | Details
31 2R7Z 7 D DNA-directed RNA polymerase II subunit RPB4 4932 2.7.7.6 | Details
32 3I4M 4 D DNA-directed RNA polymerase II subunit RPB4 4932
33 3H3V 4 E DNA-directed RNA polymerase II subunit RPB4 4932 2.7.7.6 | Details
34 5U5Q 4 D DNA-directed RNA polymerase II subunit RPB4 4932
35 5C4X 4 D DNA-directed RNA polymerase II subunit RPB4 4932
36 2VUM 4 D DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB4 4932 2.7.7.6 | Details
37 5C44 4 D DNA-directed RNA polymerase II subunit RPB4 4932
38 2R93 5 D DNA-directed RNA polymerase II subunit RPB4 4932 2.7.7.6 | Details
39 3I4N 4 D DNA-directed RNA polymerase II subunit RPB4 4932
40 4BXZ 4 D DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB4 4932 2.7.7.6 | Details
41 5C4A 4 D DNA-directed RNA polymerase II subunit RPB4 4932
42 3K1F 4 D DNA-directed RNA polymerase II subunit RPB4 4932 2.7.7.6 | Details
43 1WCM 4 D DNA-DIRECTED RNA POLYMERASE II 32 KDA POLYPEPTIDE NUMBERING OF RESIUDES D10-D24 IS ARBITRARY 4932 2.7.7.6 | Details
44 2JA7 7 D, P DNA-DIRECTED RNA POLYMERASE II 32KDA POLYPEPTIDE 4932 2.7.7.6 | Details
45 1Y1W 7 D DNA-directed RNA polymerase II 32 kDa polypeptide 4932 2.7.7.6 | Details
46 3QT1 4 D DNA-directed RNA polymerase II subunit RPB4 4932 2.7.7.6 | Details
47 2JA8 4 D DNA-DIRECTED RNA POLYMERASE II 32KDA POLYPEPTIDE 4932 2.7.7.6 | Details
48 2JA5 4 D DNA-directed RNA polymerase II subunit RPB4 4932
49 2B63 5 D DNA-directed RNA polymerase II 32 kDa polypeptide 4932 2.7.7.6 | Details
50 1Y1V 4 D DNA-directed RNA polymerase II 32 kDa polypeptide 4932 2.7.7.6 | Details
51 3FKI 4 D DNA-directed RNA polymerase II subunit RPB4 4932
52 1Y1Y 6 D DNA-directed RNA polymerase II 32 kDa polypeptide 4932 2.7.7.6 | Details
53 2JA6 4 D DNA-DIRECTED RNA POLYMERASE II 32KDA POLYPEPTIDE 4932 2.7.7.6 | Details
54 1Y77 7 D DNA-directed RNA polymerase II 32 kDa polypeptide 4932 2.7.7.6 | Details
55 2B8K 4 D DNA-directed RNA polymerase II 32 kDa polypeptide 4932 2.7.7.6 | Details
56 5OQM 4 D DNA-directed RNA polymerase II subunit RPB4 4932
57 5OQJ 4 D DNA-directed RNA polymerase II subunit RPB4 4932
58 5VVS 4 D DNA-directed RNA polymerase II subunit RPB4 4932
59 5VVR 4 D DNA-directed RNA polymerase II subunit RPB4 4932
60 5SVA 4 D DNA-directed RNA polymerase II subunit RPB4 4932
61 5FYW 4 D DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB4 4932
62 5FZ5 4 D DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB4 4932
63 5FMF 6 D RNA POLYMERASE II PRE-INITIATION COMPLEX, RPB4 4932
64 4V1N 4 D DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB4 4932
65 4V1O 4 D DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB4 4932
66 3J1N 4 D DNA-directed RNA polymerase II subunit RPB4 4932
67 3J0K 4 D DNA-directed RNA polymerase II 32 kDa polypeptide 9606 2.7.7.6 | Details
68 1PQV 4 D DNA-directed RNA polymerase II 32 kDa polypeptide 4932 2.7.7.6 | Details
69 1NT9 4 D YEAST DNA-DIRECTED RNA POLYMERASE II 32 KD POLYPEPTIDE Numbering of resiudes D10-D24 is arbitrary 4932 2.7.7.6 | Details