Sequence Similarity Clusters for the Entities in PDB 1NIK

Entity #1 | Chains: A
RPB1 protein, length: 1733 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name Structural variation in cluster
100 % 111 127 243
95 % 111 127 319 Flexibility: Low
Max RMSD: 6.8, Avg RMSD: 1.6
PDBFlex
90 % 111 127 331
70 % 113 132 357
50 % 114 147 386
40 % 114 147 415
30 % 114 147 412
Entity #10 | Chains: J
DNA-directed RNA polymerase II, chain RPB10 protein, length: 70 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name Structural variation in cluster
100 % 116 168 185
95 % 116 168 236 Flexibility: No
Max RMSD: 1.1, Avg RMSD: 0.5
PDBFlex
90 % 116 168 243
70 % 119 188 230
50 % 127 196 231
40 % 127 196 255
30 % 127 196 269
Entity #11 | Chains: K
DNA-directed RNA polymerase II, chain RPB11 protein, length: 120 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name Structural variation in cluster
100 % 111 129 237
95 % 111 129 306 Flexibility: No
Max RMSD: 1.1, Avg RMSD: 0.5
PDBFlex
90 % 111 129 318
70 % 111 129 370
50 % 113 134 418
40 % 114 136 435
30 % 114 136 436
Entity #12 | Chains: L
DNA-directed RNA polymerase II, chain RPB12 protein, length: 70 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name Structural variation in cluster
100 % 114 164 187
95 % 114 164 238 Flexibility: Low
Max RMSD: 2.0, Avg RMSD: 1.0
PDBFlex
90 % 114 164 247
70 % 114 164 273
50 % 116 169 289
40 % 116 169 320
30 % 116 169 328
Entity #2 | Chains: B
ORF YOR151c protein, length: 1224 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name Structural variation in cluster
100 % 111 129 240
95 % 111 129 313 Flexibility: Low
Max RMSD: 3.3, Avg RMSD: 1.2
PDBFlex
90 % 111 129 324
70 % 114 136 343
50 % 114 149 377
40 % 122 157 360
30 % 239 325 139
Entity #3 | Chains: C
DNA-directed RNA polymerase II, chain RPB3 protein, length: 318 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name Structural variation in cluster
100 % 109 124 251
95 % 109 124 328 Flexibility: Low
Max RMSD: 1.0, Avg RMSD: 0.5
PDBFlex
90 % 109 124 341
70 % 109 124 385
50 % 109 124 452
40 % 109 124 487
30 % 109 124 490
Entity #4 | Chains: D
DNA-directed RNA polymerase II, chain RPB4 protein, length: 161 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
Entity #5 | Chains: E
DNA-directed RNA polymerase II, chain RPB5 protein, length: 215 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name Structural variation in cluster
100 % 117 169 184
95 % 117 169 232 Flexibility: Low
Max RMSD: 2.1, Avg RMSD: 0.7
PDBFlex
90 % 117 169 240
70 % 119 174 251
50 % 120 176 270
40 % 120 189 275
30 % 120 189 287
Entity #6 | Chains: F
DNA-directed RNA polymerase 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 % 114 163 189
95 % 114 163 240 Flexibility: Low
Max RMSD: 1.4, Avg RMSD: 0.6
PDBFlex
90 % 114 163 249
70 % 114 163 277
50 % 117 184 251
40 % 117 184 278
30 % 117 184 293
Entity #7 | Chains: G
DNA-directed RNA polymerase II, chain RPB7 protein, length: 170 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
Entity #8 | Chains: H
DNA-directed RNA polymerase subunit RPB8 protein, length: 146 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name Structural variation in cluster
100 % 115 168 186
95 % 116 169 234 Flexibility: Low
Max RMSD: 1.9, Avg RMSD: 0.9
PDBFlex
90 % 116 169 241
70 % 116 169 267
50 % 118 174 278
40 % 118 174 304
30 % 119 190 286
Entity #9 | Chains: I
DNA-directed RNA polymerase II, chain RPB9 protein, length: 122 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name Structural variation in cluster
100 % 110 128 241
95 % 110 128 314 Flexibility: Low
Max RMSD: 2.9, Avg RMSD: 1.0
PDBFlex
90 % 110 128 325
70 % 112 133 351
50 % 113 135 415
40 % 113 135 440
30 % 113 150 403

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