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 % 130 130 245
95 % 130 130 313 Flexibility: Low
Max RMSD: 6.8, Avg RMSD: 1.6
PDBFlex
90 % 130 130 326
70 % 142 142 339
50 % 157 157 366
40 % 157 157 399
30 % 157 157 403
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 % 171 171 184
95 % 171 171 233 Flexibility: No
Max RMSD: 1.1, Avg RMSD: 0.5
PDBFlex
90 % 171 171 242
70 % 198 198 216
50 % 206 206 223
40 % 206 206 252
30 % 206 206 267
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 % 132 132 234
95 % 132 132 301 Flexibility: No
Max RMSD: 1.1, Avg RMSD: 0.5
PDBFlex
90 % 132 132 312
70 % 132 132 362
50 % 144 144 403
40 % 146 146 422
30 % 146 146 420
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 % 167 167 187
95 % 167 167 238 Flexibility: Low
Max RMSD: 2.0, Avg RMSD: 1.0
PDBFlex
90 % 167 167 245
70 % 167 167 280
50 % 179 179 278
40 % 179 179 313
30 % 179 179 321
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 % 132 132 237
95 % 132 132 302 Flexibility: Low
Max RMSD: 3.3, Avg RMSD: 1.2
PDBFlex
90 % 132 132 313
70 % 146 146 332
50 % 159 159 359
40 % 167 167 357
30 % 338 340 143
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 % 127 127 248
95 % 127 127 323 Flexibility: Low
Max RMSD: 1.0, Avg RMSD: 0.5
PDBFlex
90 % 127 127 336
70 % 127 127 385
50 % 127 127 453
40 % 127 127 491
30 % 127 127 496
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 % 69 69 598
95 % 69 69 736 Flexibility: Low
Max RMSD: 3.5, Avg RMSD: 0.8
PDBFlex
90 % 69 69 769
70 % 72 72 781
50 % 84 84 680
40 % 84 84 718
30 % 84 84 722
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 % 172 172 181
95 % 172 172 230 Flexibility: Low
Max RMSD: 2.1, Avg RMSD: 0.7
PDBFlex
90 % 172 172 239
70 % 184 184 241
50 % 186 186 263
40 % 199 199 270
30 % 199 199 284
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 % 166 166 188
95 % 166 166 240 Flexibility: Low
Max RMSD: 1.4, Avg RMSD: 0.6
PDBFlex
90 % 166 166 247
70 % 166 166 283
50 % 193 194 245
40 % 193 194 277
30 % 193 194 291
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 % 72 72 551
95 % 72 72 686 Flexibility: Low
Max RMSD: 4.4, Avg RMSD: 0.7
PDBFlex
90 % 72 72 708
70 % 72 72 754
50 % 100 100 519
40 % 100 100 563
30 % 100 100 573
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 % 170 171 185
95 % 171 172 231 Flexibility: Low
Max RMSD: 1.9, Avg RMSD: 0.9
PDBFlex
90 % 171 172 240
70 % 171 172 268
50 % 183 184 266
40 % 183 184 302
30 % 199 200 282
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 % 131 131 240
95 % 131 131 304 Flexibility: Low
Max RMSD: 2.9, Avg RMSD: 1.0
PDBFlex
90 % 131 131 316
70 % 143 143 336
50 % 145 145 398
40 % 145 145 423
30 % 160 160 393

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


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Rank PDB ID Entity ID Chains Description Details Taxonomy EC Number
1 1TWF 3 C DNA-directed RNA polymerase II 45 kDa polypeptide 4932 2.7.7.6 | Details
2 3S14 3 C DNA-directed RNA polymerase II subunit RPB3 4932
3 3CQZ 3 C DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB3 4932
4 3PO2 3 C DNA-directed RNA polymerase II subunit RPB3 4932 2.7.7.6 | Details
5 3RZO 3 C DNA-directed RNA polymerase II subunit RPB3 4932
6 3PO3 3 C DNA-directed RNA polymerase II subunit RPB3 4932 2.7.7.6 | Details
7 3S1M 3 C DNA-directed RNA polymerase II subunit RPB3 4932
8 4A3E 3 C DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB3 4932
9 5OT2 3 C DNA-directed RNA polymerase II subunit RPB3 4932
10 3S1R 3 C DNA-directed RNA polymerase II subunit RPB3 4932
11 4A3D 3 C DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB3 4932
12 3S1N 3 C DNA-directed RNA polymerase II subunit RPB3 4932
13 4A3F 3 C DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB3 4932
14 4A93 3 C DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB3 4932
15 1K83 3 C DNA-DIRECTED RNA POLYMERASE II 45KD POLYPEPTIDE 4932 2.7.7.6 | Details
16 1I50 3 C DNA-DIRECTED RNA POLYMERASE II 45KD POLYPEPTIDE 4932 2.7.7.6 | Details
17 4BY7 3 C DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB3 4932
18 3S2D 3 C DNA-directed RNA polymerase II subunit RPB3 4932
19 4A3C 3 C DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB3 4932
20 4A3K 3 C DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB3 4932
21 3S15 3 C DNA-directed RNA polymerase II subunit RPB3 4932
22 4A3L 3 C DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB3 4932
23 4BXX 3 C DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB3 4932
24 3S1Q 3 C DNA-directed RNA polymerase II subunit RPB3 4932
25 3S16 3 C DNA-directed RNA polymerase II subunit RPB3 4932
26 3S17 3 C DNA-directed RNA polymerase II subunit RPB3 4932
27 4A3G 3 C DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB3 4932
28 4A3B 3 C DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB3 4932
29 4BBR 3 C DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB3 4932
30 2NVQ 6 C DNA-directed RNA polymerase II 45 kDa polypeptide 4932 2.7.7.6 | Details
31 3RZD 3 C DNA-directed RNA polymerase II subunit RPB3 4932
32 4A3J 3 C DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB3 4932
33 3S2H 3 C DNA-directed RNA polymerase II subunit RPB3 4932
34 3M3Y 3 C DNA-directed RNA polymerase II subunit RPB3 4932
35 4A3I 3 C DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB3 4932
36 6BM4 3 C DNA-directed RNA polymerase II subunit RPB3 4932
37 4BY1 3 C DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB3 4932
38 4A3M 3 C DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB3 4932
39 6BLP 3 C DNA-directed RNA polymerase II subunit RPB3 4932
40 4Y7N 3 C DNA-directed RNA polymerase II subunit RPB3 4932
41 1I3Q 3 C DNA-DIRECTED RNA POLYMERASE II 45KD POLYPEPTIDE 4932 2.7.7.6 | Details
42 4BBS 3 C DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB3 4932
43 6BLO 3 C DNA-directed RNA polymerase II subunit RPB3 4932
44 1TWC 3 C DNA-directed RNA polymerase II 45 kDa polypeptide 4932 2.7.7.6 | Details
45 4Y52 3 C DNA-directed RNA polymerase II subunit RPB3 4932
46 6BQF 3 C DNA-directed RNA polymerase II subunit RPB3 4932
47 3HOU 3 C, O DNA-directed RNA polymerase II subunit RPB3 4932 2.7.7.6 | Details
48 3HOY 3 C DNA-directed RNA polymerase II subunit RPB3 4932 2.7.7.6 | Details
49 3HOV 3 C DNA-directed RNA polymerase II subunit RPB3 4932 2.7.7.6 | Details
50 6BM2 3 C DNA-directed RNA polymerase II subunit RPB3 4932
51 1TWA 3 C DNA-directed RNA polymerase II 45 kDa polypeptide 4932 2.7.7.6 | Details
52 5C3E 3 C DNA-directed RNA polymerase II subunit RPB3 4932
53 5W51 3 C DNA-directed RNA polymerase II subunit RPB3 4932
54 2NVT 6 C DNA-directed RNA polymerase II 45 kDa polypeptide 4932 2.7.7.6 | Details
55 3HOZ 3 C DNA-directed RNA polymerase II subunit RPB3 4932 2.7.7.6 | Details
56 3HOW 3 C DNA-directed RNA polymerase II subunit RPB3 4932 2.7.7.6 | Details
57 3HOX 3 C DNA-directed RNA polymerase II subunit RPB3 4932 2.7.7.6 | Details
58 1I6H 5 C DNA-DIRECTED RNA POLYMERASE II 45KD POLYPEPTIDE 4932 2.7.7.6 | Details
59 2R92 5 C DNA-directed RNA polymerase II subunit RPB3 4932 2.7.7.6 | Details
60 5W4U 3 C DNA-directed RNA polymerase II subunit RPB3 4932
61 2R7Z 6 C DNA-directed RNA polymerase II subunit RPB3 4932 2.7.7.6 | Details
62 1R9T 6 C DNA-directed RNA polymerase II 45 kDa polypeptide 4932 2.7.7.6 | Details
63 3I4M 3 C DNA-directed RNA polymerase II subunit RPB3 4932
64 3H3V 3 D DNA-directed RNA polymerase II subunit RPB3 4932 2.7.7.6 | Details
65 5U5Q 3 C DNA-directed RNA polymerase II subunit RPB3 4932
66 1TWH 3 C DNA-directed RNA polymerase II 45 kDa polypeptide 4932 2.7.7.6 | Details
67 2NVY 3 C DNA-directed RNA polymerase II 45 kDa polypeptide 4932 2.7.7.6 | Details
68 2E2J 6 C DNA-directed RNA polymerase II 45 kDa polypeptide 4932 2.7.7.6 | Details
69 5C4X 3 C DNA-directed RNA polymerase II subunit RPB3 4932
70 2VUM 3 C DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB3 4932 2.7.7.6 | Details
71 5C44 3 C DNA-directed RNA polymerase II subunit RPB3 4932
72 3M4O 3 C DNA-directed RNA polymerase II subunit RPB3 4932
73 5C4J 3 C DNA-directed RNA polymerase II subunit RPB3 4932
74 2R93 4 C DNA-directed RNA polymerase II subunit RPB3 4932 2.7.7.6 | Details
75 1TWG 3 C DNA-directed RNA polymerase II 45 kDa polypeptide 4932 2.7.7.6 | Details
76 3GTM 3 C DNA-directed RNA polymerase II subunit RPB3 DNA-directed RNA polymerase II 45 kDa polypeptide 4932
77 3I4N 3 C DNA-directed RNA polymerase II subunit RPB3 4932
78 2E2I 6 C DNA-directed RNA polymerase II 45 kDa polypeptide 4932 2.7.7.6 | Details
79 3GTL 3 C DNA-directed RNA polymerase II subunit RPB3 DNA-directed RNA polymerase II 45 kDa polypeptide 4932
80 4BXZ 3 C DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB3 4932 2.7.7.6 | Details
81 3GTK 3 C DNA-directed RNA polymerase II subunit RPB3 DNA-directed RNA polymerase II 45 kDa polypeptide 4932
82 5C4A 3 C DNA-directed RNA polymerase II subunit RPB3 4932
83 3K1F 3 C DNA-directed RNA polymerase II subunit RPB3 4932 2.7.7.6 | Details
84 3GTJ 3 C DNA-directed RNA polymerase II subunit RPB3 DNA-directed RNA polymerase II 45 kDa polypeptide 4932
85 3GTG 3 C DNA-directed RNA polymerase II subunit RPB3 DNA-directed RNA polymerase II 45 kDa polypeptide 4932
86 2YU9 6 C DNA-directed RNA polymerase II 45 kDa polypeptide 4932 2.7.7.6 | Details
87 1WCM 3 C DNA-DIRECTED RNA POLYMERASE II 45 KDA POLYPEPTIDE 4932 2.7.7.6 | Details
88 2JA7 6 C, O DNA-DIRECTED RNA POLYMERASE II 45KDA POLYPEPTIDE 4932 2.7.7.6 | Details
89 4X6A 3 C DNA-directed RNA polymerase II subunit RPB3 4932
90 4X67 3 C DNA-directed RNA polymerase II subunit RPB3 4932
91 1Y1W 6 C DNA-directed RNA polymerase II 45 kDa polypeptide 4932 2.7.7.6 | Details
92 3QT1 3 C DNA-directed RNA polymerase II subunit RPB3 4932 2.7.7.6 | Details
93 3K7A 3 C DNA-directed RNA polymerase II subunit RPB3 4932
94 2JA8 3 C DNA-DIRECTED RNA POLYMERASE II 45KDA POLYPEPTIDE 4932 2.7.7.6 | Details
95 2JA5 3 C DNA-directed RNA polymerase II subunit RPB3 4932
96 2NVX 6 C DNA-directed RNA polymerase II 45 kDa polypeptide 4932 2.7.7.6 | Details
97 2B63 4 C DNA-directed RNA polymerase II 45 kDa polypeptide 4932 2.7.7.6 | Details
98 3GTQ 3 C DNA-directed RNA polymerase II subunit RPB3 DNA-directed RNA polymerase II 45 kDa polypeptide 4932
99 3GTP 3 C DNA-directed RNA polymerase II subunit RPB3 DNA-directed RNA polymerase II 45 kDa polypeptide 4932
100 1Y1V 3 C DNA-directed RNA polymerase II 45 kDa polypeptide 4932 2.7.7.6 | Details
101 3GTO 3 C DNA-directed RNA polymerase II subunit RPB3 DNA-directed RNA polymerase II 45 kDa polypeptide 4932
102 3FKI 3 C DNA-directed RNA polymerase II subunit RPB3 4932
103 1Y1Y 5 C DNA-directed RNA polymerase II 45 kDa polypeptide 4932 2.7.7.6 | Details
104 1SFO 5 C DNA-directed RNA polymerase II 45 kDa polypeptide 4932 2.7.7.6 | Details
105 2E2H 6 C DNA-directed RNA polymerase II 45 kDa polypeptide 4932 2.7.7.6 | Details
106 2JA6 3 C DNA-DIRECTED RNA POLYMERASE II 45KDA POLYPEPTIDE 4932 2.7.7.6 | Details
107 2NVZ 6 C DNA-directed RNA polymerase II 45 kDa polypeptide 4932 2.7.7.6 | Details
108 1Y77 6 C DNA-directed RNA polymerase II 45 kDa polypeptide 4932 2.7.7.6 | Details
109 1NIK 3 C DNA-directed RNA polymerase II, chain RPB3 4932 2.7.7.6 | Details
110 1R9S 5 C DNA-directed RNA polymerase II 45 kDa polypeptide 4932 2.7.7.6 | Details
111 1R5U 3 C DNA-directed RNA polymerase II 45 kDa polypeptide 4932 2.7.7.6 | Details
112 2B8K 3 C DNA-directed RNA polymerase II 45 kDa polypeptide 4932 2.7.7.6 | Details
113 6GYK 3 C DNA-directed RNA polymerase II subunit RPB3 4932
114 6GYL 3 C DNA-directed RNA polymerase II subunit RPB3 4932
115 6GYM 11 C DNA-directed RNA polymerase II subunit RPB3 4932
116 5OQM 3 C DNA-directed RNA polymerase II subunit RPB3 4932
117 5OQJ 3 C DNA-directed RNA polymerase II subunit RPB3 4932
118 5VVS 3 C DNA-directed RNA polymerase II subunit RPB3 4932
119 5VVR 3 C DNA-directed RNA polymerase II subunit RPB3 4932
120 5SVA 3 C DNA-directed RNA polymerase II subunit RPB3 4932
121 5FYW 3 C DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB3 4932
122 5FZ5 3 C DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB3 4932
123 4V1M 3 C DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB3 4932
124 4V1N 3 C DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB3 4932
125 4V1O 3 C DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB3 4932
126 1PQV 3 C DNA-directed RNA polymerase II 45 kDa polypeptide 4932 2.7.7.6 | Details
127 1NT9 3 C DNA-directed RNA polymerase II 45 kDa polypeptide 4932 2.7.7.6 | Details