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 Structural variation in cluster
100 % 1 9 2911
95 % 1 9 3633 Flexibility: Low
Max RMSD: 1.4, Avg RMSD: 0.8
PDBFlex
90 % 1 12 2768
70 % 46 126 178
50 % 46 126 221
40 % 46 126 240
30 % 46 129 248
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 1258
95 % 8 25 1383 Flexibility: Low
Max RMSD: 3.5, Avg RMSD: 0.8
PDBFlex
90 % 236 693 3
70 % 805 2264 1
50 % 1648 4587 1
40 % 1648 4587 1
30 % 1842 5392 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 1256
95 % 8 25 1381 Flexibility: Low
Max RMSD: 3.8, Avg RMSD: 1.0
PDBFlex
90 % 8 25 1404
70 % 794 2222 2
50 % 1649 4587 1
40 % 1649 4587 1
30 % 1843 5392 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 24145
95 % 1 2 20591 Flexibility: Low
Max RMSD: 0.8, Avg RMSD: 0.6
PDBFlex
90 % 1 2 20015
70 % 6 15 1843
50 % 6 15 1860
40 % 6 15 1866
30 % 6 15 1805

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.