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 3211
95 % 6 11 3395 Flexibility: Low
Max RMSD: 1.4, Avg RMSD: 0.9
PDBFlex
90 % 6 13 2820
70 % 78 179 134
50 % 78 179 164
40 % 78 179 178
30 % 78 182 195
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 1522
95 % 19 34 1082 Flexibility: Low
Max RMSD: 3.5, Avg RMSD: 0.8
PDBFlex
90 % 471 762 2
70 % 1550 2519 1
50 % 3152 5107 1
40 % 3586 5756 1
30 % 4438 7175 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 % 15 24 1314
95 % 16 25 1454 Flexibility: Low
Max RMSD: 3.9, Avg RMSD: 1.0
PDBFlex
90 % 16 25 1481
70 % 1524 2478 2
50 % 3153 5107 1
40 % 3587 5756 1
30 % 4439 7175 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 % 4 4 9426
95 % 9 15 1830 Flexibility: Low
Max RMSD: 0.8, Avg RMSD: 0.6
PDBFlex
90 % 9 15 1868
70 % 9 15 1883
50 % 9 16 1834
40 % 9 16 1821
30 % 9 16 1768

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