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 % 118 118 236
95 % 118 118 325 Flexibility: Low
Max RMSD: 5.3, Avg RMSD: 1.6
PDBFlex
90 % 118 118 343
70 % 123 123 368
50 % 135 135 386
40 % 135 135 416
30 % 135 135 414
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 % 153 153 176
95 % 153 153 239 Flexibility: No
Max RMSD: 1.1, Avg RMSD: 0.5
PDBFlex
90 % 153 153 251
70 % 170 170 246
50 % 178 178 236
40 % 178 178 255
30 % 178 178 264
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 % 120 120 231
95 % 120 120 320 Flexibility: No
Max RMSD: 1.0, Avg RMSD: 0.5
PDBFlex
90 % 120 120 337
70 % 120 120 379
50 % 125 125 429
40 % 127 127 442
30 % 127 127 444
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 % 149 149 181
95 % 149 149 242 Flexibility: Low
Max RMSD: 2.0, Avg RMSD: 1.0
PDBFlex
90 % 149 149 255
70 % 149 149 291
50 % 154 154 306
40 % 154 154 325
30 % 154 154 329
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 % 119 119 232
95 % 120 120 319 Flexibility: Low
Max RMSD: 3.3, Avg RMSD: 1.3
PDBFlex
90 % 120 120 335
70 % 127 127 351
50 % 137 137 377
40 % 145 145 348
30 % 156 156 317
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 % 115 115 238
95 % 115 115 333 Flexibility: Low
Max RMSD: 1.0, Avg RMSD: 0.5
PDBFlex
90 % 115 115 353
70 % 115 115 389
50 % 117 117 449
40 % 117 117 479
30 % 117 117 471
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 % 64 64 557
95 % 64 64 753 Flexibility: Low
Max RMSD: 3.5, Avg RMSD: 0.7
PDBFlex
90 % 64 64 783
70 % 65 65 817
50 % 72 72 741
40 % 72 72 778
30 % 72 72 771
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 % 154 154 172
95 % 154 154 234 Flexibility: Low
Max RMSD: 2.1, Avg RMSD: 0.7
PDBFlex
90 % 154 154 246
70 % 159 159 268
50 % 161 161 285
40 % 171 171 274
30 % 171 171 284
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 % 148 148 182
95 % 148 148 245 Flexibility: Low
Max RMSD: 1.4, Avg RMSD: 0.6
PDBFlex
90 % 148 148 258
70 % 148 148 293
50 % 165 166 274
40 % 165 166 288
30 % 165 166 299
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 % 67 67 500
95 % 67 67 693 Flexibility: Low
Max RMSD: 4.2, Avg RMSD: 0.7
PDBFlex
90 % 67 67 724
70 % 67 67 765
50 % 85 85 571
40 % 85 85 608
30 % 85 85 598
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 % 152 153 175
95 % 153 154 235 Flexibility: Low
Max RMSD: 1.9, Avg RMSD: 1.0
PDBFlex
90 % 153 154 247
70 % 153 154 281
50 % 158 159 289
40 % 158 159 309
30 % 171 172 282
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 % 119 119 235
95 % 119 119 322 Flexibility: Low
Max RMSD: 2.9, Avg RMSD: 1.0
PDBFlex
90 % 119 119 340
70 % 124 124 367
50 % 126 126 419
40 % 126 126 447
30 % 137 137 405

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 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 2JA7 7 D, P DNA-DIRECTED RNA POLYMERASE II 32KDA POLYPEPTIDE 4932 2.7.7.6 | Details
44 1Y1W 7 D DNA-directed RNA polymerase II 32 kDa polypeptide 4932 2.7.7.6 | Details
45 3QT1 4 D DNA-directed RNA polymerase II subunit RPB4 4932 2.7.7.6 | Details
46 2JA8 4 D DNA-DIRECTED RNA POLYMERASE II 32KDA POLYPEPTIDE 4932 2.7.7.6 | Details
47 2JA5 4 D DNA-directed RNA polymerase II subunit RPB4 4932
48 2B63 5 D DNA-directed RNA polymerase II 32 kDa polypeptide 4932 2.7.7.6 | Details
49 1Y1V 4 D DNA-directed RNA polymerase II 32 kDa polypeptide 4932 2.7.7.6 | Details
50 3FKI 4 D DNA-directed RNA polymerase II subunit RPB4 4932
51 1Y1Y 6 D DNA-directed RNA polymerase II 32 kDa polypeptide 4932 2.7.7.6 | Details
52 2JA6 4 D DNA-DIRECTED RNA POLYMERASE II 32KDA POLYPEPTIDE 4932 2.7.7.6 | Details
53 1Y77 7 D DNA-directed RNA polymerase II 32 kDa polypeptide 4932 2.7.7.6 | Details
54 2B8K 4 D DNA-directed RNA polymerase II 32 kDa polypeptide 4932 2.7.7.6 | Details
55 5VVS 4 D DNA-directed RNA polymerase II subunit RPB4 4932
56 5VVR 4 D DNA-directed RNA polymerase II subunit RPB4 4932
57 5SVA 4 D DNA-directed RNA polymerase II subunit RPB4 4932
58 5FYW 4 D DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB4 4932
59 5FZ5 4 D DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB4 4932
60 4V1N 4 D DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB4 4932
61 4V1O 4 D DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB4 4932
62 3J1N 4 D DNA-directed RNA polymerase II subunit RPB4 4932
63 3J0K 4 D DNA-directed RNA polymerase II 32 kDa polypeptide 9606 2.7.7.6 | Details
64 1PQV 4 D DNA-directed RNA polymerase II 32 kDa polypeptide 4932 2.7.7.6 | Details
65 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