Sequence Similarity Clusters for the Entities in PDB 2HMI

Entity #1 | Chains: E
DNA (5'-D(*AP*TP*GP*GP*CP*GP*CP*CP*CP*GP*AP*AP*CP*AP*GP*GP*GP*AP*C)-3') dna, length: 19 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
Entity #2 | Chains: F
DNA (5'-D(*GP*TP*CP*CP*CP*TP*GP*TP*TP*CP*GP*GP*GP*CP*GP*CP*CP*A)-3') dna, length: 18 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
Entity #3 | Chains: A
SUBUNIT OF V-1 REVERSE TRANSCRIPTASE protein, length: 558 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name Structural variation in cluster
100 % 19 26 1200
95 % 214 252 92 Flexibility: Medium
Max RMSD: 23.3, Avg RMSD: 3.9
PDBFlex
90 % 214 252 97
70 % 214 252 114
50 % 215 253 152
40 % 216 254 165
30 % 216 254 179
Entity #4 | Chains: B
HISUBUNIT OF V-1 REVERSE TRANSCRIPTASE protein, length: 430 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 87 105 206
95 % 209 246 116
90 % 209 246 120
70 % 209 246 136
50 % 211 248 159
40 % 211 248 176
30 % 211 248 187
Entity #5 | Chains: C
FAB FRAGMENT OF MONOCLONAL ANTIBODY 28 protein, length: 214 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name Structural variation in cluster
100 % 1 2 41445
95 % 1 3 23483 Flexibility: No
Max RMSD: 0.4, Avg RMSD: 0.4
PDBFlex
90 % 56 68 377
70 % 2004 2392 1
50 % 4064 4843 1
40 % 4064 4843 1
30 % 4817 5705 1
Entity #6 | Chains: D
FAB FRAGMENT OF MONOCLONAL ANTIBODY 28 protein, length: 220 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name Structural variation in cluster
100 % 1 3 28001
95 % 3 8 9368 Flexibility: Low
Max RMSD: 0.7, Avg RMSD: 0.6
PDBFlex
90 % 3 8 9273
70 % 1962 2342 2
50 % 4065 4843 1
40 % 4065 4843 1
30 % 4818 5705 1

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