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 2913
95 % 1 10 3621
90 % 1 13 2812
70 % 46 130 184
50 % 46 130 225
40 % 46 130 242
30 % 46 133 251
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 1354
95 % 10 32 1175 Flexibility: Low
Max RMSD: 3.5, Avg RMSD: 0.8
PDBFlex
90 % 284 788 2
70 % 900 2474 1
50 % 1838 5011 1
40 % 1838 5011 1
30 % 2094 5941 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 1352
95 % 8 25 1467 Flexibility: Low
Max RMSD: 3.9, Avg RMSD: 1.0
PDBFlex
90 % 8 25 1493
70 % 885 2424 2
50 % 1839 5011 1
40 % 1839 5011 1
30 % 2095 5941 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 25697
95 % 1 2 21870 Flexibility: Low
Max RMSD: 0.8, Avg RMSD: 0.6
PDBFlex
90 % 1 2 21222
70 % 6 16 1820
50 % 6 16 1855
40 % 6 16 1856
30 % 6 16 1795

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