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 % 5 10 2818
95 % 5 10 3512 Flexibility: Low
Max RMSD: 1.4, Avg RMSD: 0.9
PDBFlex
90 % 6 13 2725
70 % 76 128 181
50 % 76 128 223
40 % 76 128 241
30 % 76 131 249
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 1304
95 % 18 32 1137 Flexibility: Low
Max RMSD: 3.5, Avg RMSD: 0.8
PDBFlex
90 % 446 729 3
70 % 1456 2362 1
50 % 2956 4781 1
40 % 2956 4781 1
30 % 3429 5635 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 1302
95 % 16 25 1417 Flexibility: Low
Max RMSD: 3.9, Avg RMSD: 1.0
PDBFlex
90 % 16 25 1441
70 % 1426 2311 2
50 % 2957 4781 1
40 % 2957 4781 1
30 % 3430 5635 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 24873
95 % 2 2 21227 Flexibility: Low
Max RMSD: 0.8, Avg RMSD: 0.6
PDBFlex
90 % 2 2 20624
70 % 9 16 1741
50 % 9 16 1786
40 % 9 16 1794
30 % 9 16 1736

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