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 % 20 27 1194
95 % 218 256 112 Flexibility: Medium
Max RMSD: 23.3, Avg RMSD: 3.9
PDBFlex
90 % 218 256 117
70 % 218 256 130
50 % 219 257 157
40 % 220 258 168
30 % 220 258 179
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 % 88 106 209
95 % 213 250 118
90 % 213 250 122
70 % 213 250 137
50 % 215 252 164
40 % 215 252 175
30 % 215 252 187
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 42261
95 % 1 3 23941 Flexibility: No
Max RMSD: 0.4, Avg RMSD: 0.4
PDBFlex
90 % 56 68 398
70 % 2069 2474 1
50 % 4198 5011 1
40 % 4198 5011 1
30 % 5017 5941 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 28584
95 % 3 8 9579 Flexibility: Low
Max RMSD: 0.7, Avg RMSD: 0.6
PDBFlex
90 % 3 8 9482
70 % 2027 2424 2
50 % 4199 5011 1
40 % 4199 5011 1
30 % 5018 5941 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