Sequence Similarity Clusters for the Entities in PDB 1Y1Y

Entity #1 | Chains: T
5'-D(P*TP*AP*CP*GP*CP*CP*T)-3' dna, length: 7 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
Entity #10 | Chains: H
DNA-directed RNA polymerases I, II, and III 14.5 kDa polypeptide protein, length: 146 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name Structural variation in cluster
100 % 107 160 184
95 % 108 161 234 Flexibility: Low
Max RMSD: 1.9, Avg RMSD: 0.9
PDBFlex
90 % 108 161 241
70 % 108 161 274
50 % 110 166 286
40 % 110 166 319
30 % 111 180 293
Entity #11 | Chains: I
DNA-directed RNA polymerase II subunit 9 protein, length: 122 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name Structural variation in cluster
100 % 102 126 237
95 % 102 126 314 Flexibility: Low
Max RMSD: 2.9, Avg RMSD: 1.0
PDBFlex
90 % 102 126 325
70 % 104 131 348
50 % 105 133 404
40 % 105 133 434
30 % 105 144 405
Entity #12 | Chains: J
DNA-directed RNA polymerases I/II/III subunit 10 protein, length: 70 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name Structural variation in cluster
100 % 108 160 183
95 % 108 160 236 Flexibility: No
Max RMSD: 1.1, Avg RMSD: 0.5
PDBFlex
90 % 108 160 242
70 % 111 178 235
50 % 116 186 232
40 % 116 186 258
30 % 116 186 275
Entity #13 | Chains: K
DNA-directed RNA polymerase II 13.6 kDa polypeptide protein, length: 120 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name Structural variation in cluster
100 % 103 127 232
95 % 103 127 309 Flexibility: No
Max RMSD: 1.1, Avg RMSD: 0.5
PDBFlex
90 % 103 127 320
70 % 103 127 369
50 % 105 132 413
40 % 106 134 428
30 % 106 134 436
Entity #14 | 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 % 106 156 187
95 % 106 156 242 Flexibility: Low
Max RMSD: 2.0, Avg RMSD: 1.0
PDBFlex
90 % 106 156 250
70 % 106 156 283
50 % 108 161 301
40 % 108 161 330
30 % 108 161 336
Entity #15 | Chains: S
Transcription elongation factor S-II protein, length: 179 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name Structural variation in cluster
100 % 2 3 27394
95 % 4 5 14937 Flexibility: Low
Max RMSD: 2.8, Avg RMSD: 1.9
PDBFlex
90 % 4 5 15483
70 % 4 5 14478
50 % 4 6 10466
40 % 4 6 9453
30 % 4 6 8103
Entity #2 | Chains: P
5'-R(P*AP*GP*GP*C)-3' rna, length: 4 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
Entity #3 | 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 % 103 125 242
95 % 103 125 320 Flexibility: Low
Max RMSD: 6.8, Avg RMSD: 1.6
PDBFlex
90 % 103 125 330
70 % 105 130 352
50 % 106 143 383
40 % 106 143 411
30 % 106 143 409
Entity #4 | Chains: B
DNA-directed RNA polymerase II 140 kDa polypeptide protein, length: 1224 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name Structural variation in cluster
100 % 103 127 234
95 % 103 127 310 Flexibility: Low
Max RMSD: 3.3, Avg RMSD: 1.2
PDBFlex
90 % 103 127 321
70 % 106 134 336
50 % 106 145 375
40 % 111 153 360
30 % 209 306 143
Entity #5 | 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 % 101 122 246
95 % 101 122 327 Flexibility: Low
Max RMSD: 1.0, Avg RMSD: 0.5
PDBFlex
90 % 101 122 340
70 % 101 122 382
50 % 101 122 453
40 % 101 122 481
30 % 101 122 485
Entity #6 | Chains: D
DNA-directed RNA polymerase II 32 kDa polypeptide protein, length: 221 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name Structural variation in cluster
100 % 51 66 600
95 % 51 66 737 Flexibility: Low
Max RMSD: 3.5, Avg RMSD: 0.8
PDBFlex
90 % 51 66 761
70 % 52 69 767
50 % 54 74 748
40 % 54 74 778
30 % 54 74 781
Entity #7 | 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 % 109 161 182
95 % 109 161 235 Flexibility: Low
Max RMSD: 2.1, Avg RMSD: 0.7
PDBFlex
90 % 109 161 240
70 % 111 166 259
50 % 112 168 276
40 % 112 179 282
30 % 112 179 295
Entity #8 | 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 % 106 155 188
95 % 106 155 243 Flexibility: Low
Max RMSD: 1.4, Avg RMSD: 0.6
PDBFlex
90 % 106 155 251
70 % 106 155 285
50 % 109 174 262
40 % 109 174 289
30 % 109 174 300
Entity #9 | Chains: G
DNA-directed RNA polymerase II 19 kDa polypeptide protein, length: 171 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name Structural variation in cluster
100 % 53 69 539
95 % 53 69 674 Flexibility: Low
Max RMSD: 4.4, Avg RMSD: 0.7
PDBFlex
90 % 53 69 699
70 % 53 69 741
50 % 57 88 560
40 % 57 88 601
30 % 57 88 603

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 1TWF 2 B DNA-directed RNA polymerase II 140 kDa polypeptide 4932 2.7.7.6 | Details
2 3S14 2 B DNA-directed RNA polymerase II subunit RPB2 4932 2.7.7.6 | Details
3 3CQZ 2 B DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB2 4932 2.7.7.6 | Details
4 3PO2 2 B DNA-directed RNA polymerase II subunit RPB2 4932 2.7.7.6 | Details
5 3RZO 2 B DNA-directed RNA polymerase II subunit RPB2 4932 2.7.7.6 | Details
6 3PO3 2 B DNA-directed RNA polymerase II subunit RPB2 4932 2.7.7.6 | Details
7 5XOG 2 B DNA-directed RNA polymerase subunit beta 460519 2.7.7.6 | Details
8 3S1M 2 B DNA-directed RNA polymerase II subunit RPB2 4932 2.7.7.6 | Details
9 4A3E 2 B DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB2 4932 2.7.7.6 | Details
10 5OT2 2 B DNA-directed RNA polymerase II subunit RPB2 4932 2.7.7.6 | Details
11 3S1R 2 B DNA-directed RNA polymerase II subunit RPB2 4932 2.7.7.6 | Details
12 4A3D 2 B DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB2 4932 2.7.7.6 | Details
13 3S1N 2 B DNA-directed RNA polymerase II subunit RPB2 4932 2.7.7.6 | Details
14 5IP7 2 B DNA-directed RNA polymerase II subunit RPB2 4932 2.7.7.6 | Details
15 4A3F 2 B DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB2 4932 2.7.7.6 | Details
16 4A93 2 B DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB2 4932 2.7.7.6 | Details
17 1K83 2 B DNA-DIRECTED RNA POLYMERASE II 140KD POLYPEPTIDE 4932 2.7.7.6 | Details
18 1I50 2 B DNA-DIRECTED RNA POLYMERASE II 140KD POLYPEPTIDE 4932 2.7.7.6 | Details
19 4BY7 2 B DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB2 4932 2.7.7.6 | Details
20 3S2D 2 B DNA-directed RNA polymerase II subunit RPB2 4932 2.7.7.6 | Details
21 4A3C 2 B DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB2 4932 2.7.7.6 | Details
22 4A3K 2 B DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB2 4932 2.7.7.6 | Details
23 3S15 2 B DNA-directed RNA polymerase II subunit RPB2 4932 2.7.7.6 | Details
24 4A3L 2 B DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB2 4932 2.7.7.6 | Details
25 4BXX 2 B DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB2 4932 2.7.7.6 | Details
26 3S1Q 2 B DNA-directed RNA polymerase II subunit RPB2 4932 2.7.7.6 | Details
27 3S16 2 B DNA-directed RNA polymerase II subunit RPB2 4932 2.7.7.6 | Details
28 3S17 2 B DNA-directed RNA polymerase II subunit RPB2 4932 2.7.7.6 | Details
29 4A3G 2 B DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB2 4932 2.7.7.6 | Details
30 4A3B 2 B DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB2 4932 2.7.7.6 | Details
31 4BBR 2 B DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB2 4932 2.7.7.6 | Details
32 2NVQ 5 B DNA-directed RNA polymerase II 140 kDa polypeptide 4932 2.7.7.6 | Details
33 3RZD 2 B DNA-directed RNA polymerase II subunit RPB2 4932 2.7.7.6 | Details
34 4A3J 2 B DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB2 4932 2.7.7.6 | Details
35 3S2H 2 B DNA-directed RNA polymerase II subunit RPB2 4932 2.7.7.6 | Details
36 3M3Y 2 B DNA-directed RNA polymerase II subunit RPB2 4932 2.7.7.6 | Details
37 4A3I 2 B DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB2 4932 2.7.7.6 | Details
38 6BM4 2 B DNA-directed RNA polymerase II subunit RPB2 4932 2.7.7.6 | Details
39 4BY1 2 B DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB2 4932 2.7.7.6 | Details
40 4A3M 2 B DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB2 4932 2.7.7.6 | Details
41 6BLP 2 B DNA-directed RNA polymerase II subunit RPB2 4932 2.7.7.6 | Details
42 4Y7N 2 B DNA-directed RNA polymerase II subunit RPB2,DNA-directed RNA polymerase II subunit RPB2 4932 2.7.7.6 | Details
43 5IP9 2 B DNA-directed RNA polymerase II subunit RPB2 4932 2.7.7.6 | Details
44 1I3Q 2 B DNA-DIRECTED RNA POLYMERASE II 140KD POLYPEPTIDE 4932 2.7.7.6 | Details
45 4BBS 2 B DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB2 4932 2.7.7.6 | Details
46 6BLO 2 B DNA-directed RNA polymerase II subunit RPB2 4932 2.7.7.6 | Details
47 1TWC 2 B DNA-directed RNA polymerase II 140 kDa polypeptide 4932 2.7.7.6 | Details
48 4Y52 2 B DNA-directed RNA polymerase II subunit RPB2 4932 2.7.7.6 | Details
49 6BQF 2 B DNA-directed RNA polymerase II subunit RPB2 4932 2.7.7.6 | Details
50 3HOU 2 B, N DNA-directed RNA polymerase II subunit RPB2 4932 2.7.7.6 | Details
51 3HOY 2 B DNA-directed RNA polymerase II subunit RPB2 4932 2.7.7.6 | Details
52 3HOV 2 B DNA-directed RNA polymerase II subunit RPB2 4932 2.7.7.6 | Details
53 6BM2 2 B DNA-directed RNA polymerase II subunit RPB2 4932 2.7.7.6 | Details
54 1TWA 2 B DNA-directed RNA polymerase II 140 kDa polypeptide 4932 2.7.7.6 | Details
55 5C3E 2 B DNA-directed RNA polymerase II subunit RPB2 4932 2.7.7.6 | Details
56 2NVT 5 B DNA-directed RNA polymerase II 140 kDa polypeptide 4932 2.7.7.6 | Details
57 3HOZ 2 B DNA-directed RNA polymerase II subunit RPB2 4932 2.7.7.6 | Details
58 3HOW 2 B DNA-directed RNA polymerase II subunit RPB2 4932 2.7.7.6 | Details
59 3HOX 2 B DNA-directed RNA polymerase II subunit RPB2 4932 2.7.7.6 | Details
60 1I6H 4 B DNA-DIRECTED RNA POLYMERASE II 140KD POLYPEPTIDE 4932 2.7.7.6 | Details
61 2R92 4 B DNA-directed RNA polymerase II subunit RPB2 4932 2.7.7.6 | Details
62 2R7Z 5 B DNA-directed RNA polymerase II subunit RPB2 4932 2.7.7.6 | Details
63 1R9T 5 B DNA-directed RNA polymerase II 140 kDa polypeptide 4932 2.7.7.6 | Details
64 3I4M 2 B DNA-directed RNA polymerase II subunit RPB2 4932 2.7.7.6 | Details
65 3H3V 2 C DNA-directed RNA polymerase II subunit RPB2 4932 2.7.7.6 | Details
66 5U5Q 2 B DNA-directed RNA polymerase II subunit RPB2 4932 2.7.7.6 | Details
67 1TWH 2 B DNA-directed RNA polymerase II 140 kDa polypeptide 4932 2.7.7.6 | Details
68 2NVY 2 B DNA-directed RNA polymerase II 140 kDa polypeptide 4932 2.7.7.6 | Details
69 2E2J 5 B DNA-directed RNA polymerase II 140 kDa polypeptide 4932 2.7.7.6 | Details
70 5C4X 2 B DNA-directed RNA polymerase II subunit RPB2 4932 2.7.7.6 | Details
71 2VUM 2 B DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB2 4932 2.7.7.6 | Details
72 5C44 2 B DNA-directed RNA polymerase II subunit RPB2 4932 2.7.7.6 | Details
73 3M4O 2 B DNA-directed RNA polymerase II subunit RPB2 4932 2.7.7.6 | Details
74 5C4J 2 B DNA-directed RNA polymerase II subunit RPB2 4932 2.7.7.6 | Details
75 2R93 3 B DNA-directed RNA polymerase II subunit RPB2 4932 2.7.7.6 | Details
76 1TWG 2 B DNA-directed RNA polymerase II 140 kDa polypeptide 4932 2.7.7.6 | Details
77 3GTM 2 B DNA-directed RNA polymerase II subunit RPB2 DNA-directed RNA polymerase II 140 kDa polypeptide 4932 2.7.7.6 | Details
78 3I4N 2 B DNA-directed RNA polymerase II subunit RPB2 4932 2.7.7.6 | Details
79 2E2I 5 B DNA-directed RNA polymerase II 140 kDa polypeptide 4932 2.7.7.6 | Details
80 3GTL 2 B DNA-directed RNA polymerase II subunit RPB2 DNA-directed RNA polymerase II 140 kDa polypeptide 4932 2.7.7.6 | Details
81 4BXZ 2 B DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB2 4932 2.7.7.6 | Details
82 3GTK 2 B DNA-directed RNA polymerase II subunit RPB2 DNA-directed RNA polymerase II 140 kDa polypeptide 4932 2.7.7.6 | Details
83 5C4A 2 B DNA-directed RNA polymerase II subunit RPB2 4932 2.7.7.6 | Details
84 3K1F 2 B DNA-directed RNA polymerase II subunit RPB2 4932 2.7.7.6 | Details
85 3GTJ 2 B DNA-directed RNA polymerase II subunit RPB2 DNA-directed RNA polymerase II 140 kDa polypeptide 4932 2.7.7.6 | Details
86 3GTG 2 B DNA-directed RNA polymerase II subunit RPB2 DNA-directed RNA polymerase II 140 kDa polypeptide 4932 2.7.7.6 | Details
87 2YU9 5 B DNA-directed RNA polymerase II 140 kDa polypeptide 4932 2.7.7.6 | Details
88 1WCM 2 B DNA-DIRECTED RNA POLYMERASE II SECOND LARGEST SUBUNIT 4932 2.7.7.6 | Details
89 2JA7 5 B, N DNA-DIRECTED RNA POLYMERASE II 140 KDA POLYPEPTIDE 4932 2.7.7.6 | Details
90 4X6A 2 B DNA-directed RNA polymerase II subunit RPB2 4932 2.7.7.6 | Details
91 4X67 2 B DNA-directed RNA polymerase II subunit RPB2 4932 2.7.7.6 | Details
92 1Y1W 5 B DNA-directed RNA polymerase II 140 kDa polypeptide 4932 2.7.7.6 | Details
93 3QT1 2 B DNA-directed RNA polymerase II subunit RPB2 4932 2.7.7.6 | Details
94 3K7A 2 B DNA-directed RNA polymerase II subunit RPB2 4932 2.7.7.6 | Details
95 5X50 2 B DNA-directed RNA polymerase subunit beta 460519 2.7.7.6 | Details
96 2JA8 2 B DNA-DIRECTED RNA POLYMERASE II 140 KDA POLYPEPTIDE 4932 2.7.7.6 | Details
97 2JA5 2 B DNA-directed RNA polymerase II subunit RPB2 4932 2.7.7.6 | Details
98 2NVX 5 B DNA-directed RNA polymerase II 140 kDa polypeptide 4932 2.7.7.6 | Details
99 2B63 3 B DNA-directed RNA polymerase II 140 kDa polypeptide 4932 2.7.7.6 | Details
100 3GTQ 2 B DNA-directed RNA polymerase II subunit RPB2 DNA-directed RNA polymerase II 140 kDa polypeptide 4932 2.7.7.6 | Details
101 3GTP 2 B DNA-directed RNA polymerase II subunit RPB2 DNA-directed RNA polymerase II 140 kDa polypeptide 4932 2.7.7.6 | Details
102 1Y1V 2 B DNA-directed RNA polymerase II 140 kDa polypeptide 4932 2.7.7.6 | Details
103 3GTO 2 B DNA-directed RNA polymerase II subunit RPB2 DNA-directed RNA polymerase II 140 kDa polypeptide 4932 2.7.7.6 | Details
104 3H0G 2 B, N DNA-directed RNA polymerase II subunit RPB2 4896 2.7.7.6 | Details
105 3FKI 2 B DNA-directed RNA polymerase II subunit RPB2 4932 2.7.7.6 | Details
106 1Y1Y 4 B DNA-directed RNA polymerase II 140 kDa polypeptide 4932 2.7.7.6 | Details
107 1SFO 4 B DNA-directed RNA polymerase II 140 kDa polypeptide 4932 2.7.7.6 | Details
108 2E2H 5 B DNA-directed RNA polymerase II 140 kDa polypeptide 4932 2.7.7.6 | Details
109 2JA6 2 B DNA-DIRECTED RNA POLYMERASE II 140 KDA POLYPEPTIDE 4932 2.7.7.6 | Details
110 2NVZ 5 B DNA-directed RNA polymerase II 140 kDa polypeptide 4932 2.7.7.6 | Details
111 1Y77 5 B DNA-directed RNA polymerase II 140 kDa polypeptide 4932 2.7.7.6 | Details
112 1NIK 2 B ORF YOR151c 4932 2.7.7.6 | Details
113 1R9S 4 B DNA-directed RNA polymerase II 140 kDa polypeptide 4932 2.7.7.6 | Details
114 1R5U 2 B DNA-directed RNA polymerase II 140 kDa polypeptide 4932 2.7.7.6 | Details
115 2B8K 2 B DNA-directed RNA polymerase II 140 kDa polypeptide 4932 2.7.7.6 | Details
116 5X51 2 B, N DNA-directed RNA polymerase subunit beta 460519 2.7.7.6 | Details
117 5X4Z 2 B, N DNA-directed RNA polymerase subunit beta 460519 2.7.7.6 | Details
118 5OQM 2 B DNA-directed RNA polymerase II subunit RPB2 4932 2.7.7.6 | Details
119 5OQJ 2 B DNA-directed RNA polymerase II subunit RPB2 4932 2.7.7.6 | Details
120 5XON 2 B DNA-directed RNA polymerase subunit beta 460519 2.7.7.6 | Details
121 5VVS 2 B DNA-directed RNA polymerase II subunit RPB2 4932 2.7.7.6 | Details
122 5VVR 2 B DNA-directed RNA polymerase II subunit RPB2 4932 2.7.7.6 | Details
123 5U0S 18 b RNA polymerase II subunit Rpb2 4896 2.7.7.6 | Details
124 5SVA 2 B DNA-directed RNA polymerase II subunit RPB2 4932 2.7.7.6 | Details
125 5FYW 2 B DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB2 4932 2.7.7.6 | Details
126 5FZ5 2 B DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB2 4932 2.7.7.6 | Details
127 5FMF 4 B DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB2 4932 2.7.7.6 | Details
128 4V1M 2 B DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB2 4932 2.7.7.6 | Details
129 4V1N 2 B DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB2 4932 2.7.7.6 | Details
130 4V1O 2 B DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB2 4932 2.7.7.6 | Details
131 3J1N 2 B DNA-directed RNA polymerase II subunit RPB2 4932 2.7.7.6 | Details
132 3J0K 2 B DNA-directed RNA polymerase II 140 kDa polypeptide 9606 2.7.7.6 | Details
133 1PQV 2 B DNA-directed RNA polymerase II 140 kDa polypeptide 4932 2.7.7.6 | Details
134 1NT9 2 B DNA-directed polymerase II SECOND LARGEST SUBUNIT 4932 2.7.7.6 | Details