Sequence Similarity Clusters for the Entities in PDB 1YYL

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 % 4 9 2861
95 % 4 9 3584 Flexibility: Low
Max RMSD: 1.4, Avg RMSD: 0.8
PDBFlex
90 % 5 12 2731
70 % 75 126 179
50 % 75 126 219
40 % 75 126 241
30 % 75 129 246
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 % 14 21 1224
95 % 16 24 1485 Flexibility: Low
Max RMSD: 3.5, Avg RMSD: 0.7
PDBFlex
90 % 413 676 3
70 % 1139 1828 2
50 % 2793 4501 1
40 % 2793 4501 1
30 % 3237 5303 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 % 14 21 1222
95 % 16 24 1483 Flexibility: Low
Max RMSD: 2.3, Avg RMSD: 0.8
PDBFlex
90 % 16 24 1510
70 % 1351 2178 1
50 % 2794 4501 1
40 % 2794 4501 1
30 % 3238 5303 1
Entity #4 | Chains: M,S
CD4M33, scorpion-toxin mimic of CD4 protein, length: 27 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name Structural variation in cluster
100 % 2 2 23867
95 % 2 2 20368 Flexibility: Low
Max RMSD: 0.8, Avg RMSD: 0.6
PDBFlex
90 % 2 2 19806
70 % 9 15 1811
50 % 9 15 1831
40 % 9 15 1840
30 % 9 15 1782

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.