Sequence Similarity Clusters for the Entities in PDB 1YYM

Entity #1 | Chains: G,P
Exterior membrane glycoprotein(GP120),Exterior membrane glycoprotein(GP120),Exterior membrane glycoprotein(GP120) protein, length: 313 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 1 10 2850
95 % 1 10 3545
90 % 1 13 2750
70 % 46 129 182
50 % 46 129 223
40 % 46 129 241
30 % 46 132 248
Entity #2 | Chains: L,Q
antibody 17b light chain protein, length: 214 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name Structural variation in cluster
100 % 8 21 1315
95 % 10 32 1148 Flexibility: Low
Max RMSD: 3.5, Avg RMSD: 0.8
PDBFlex
90 % 263 746 3
70 % 861 2392 1
50 % 1759 4843 1
40 % 1759 4843 1
30 % 1973 5705 1
Entity #3 | Chains: H,R
antibody 17b heavy chain protein, length: 229 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name Structural variation in cluster
100 % 8 21 1313
95 % 8 25 1428 Flexibility: Low
Max RMSD: 3.9, Avg RMSD: 1.0
PDBFlex
90 % 8 25 1456
70 % 846 2342 2
50 % 1760 4843 1
40 % 1760 4843 1
30 % 1974 5705 1
Entity #4 | Chains: M,S
F23, scorpion-toxin mimic of CD4 protein, length: 27 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name Structural variation in cluster
100 % 1 2 25146
95 % 1 2 21434 Flexibility: Low
Max RMSD: 0.8, Avg RMSD: 0.6
PDBFlex
90 % 1 2 20814
70 % 6 16 1763
50 % 6 16 1806
40 % 6 16 1814
30 % 6 16 1753

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