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 10 3222
95 % 1 11 3413 Flexibility: Low
Max RMSD: 1.9, Avg RMSD: 1.0
PDBFlex
90 % 1 13 2835
70 % 46 180 135
50 % 46 180 164
40 % 46 180 177
30 % 46 183 194
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 1536
95 % 11 34 1093 Flexibility: Low
Max RMSD: 5.3, Avg RMSD: 1.1
PDBFlex
90 % 285 780 2
70 % 920 2553 1
50 % 1884 5180 1
40 % 2175 5834 1
30 % 2640 7269 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 24 1336
95 % 8 25 1467 Flexibility: Low
Max RMSD: 3.9, Avg RMSD: 1.0
PDBFlex
90 % 8 25 1490
70 % 908 2511 2
50 % 1885 5180 1
40 % 2176 5834 1
30 % 2641 7269 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 4 9486
95 % 6 15 1843 Flexibility: Low
Max RMSD: 0.8, Avg RMSD: 0.6
PDBFlex
90 % 6 15 1881
70 % 6 15 1897
50 % 6 16 1845
40 % 6 16 1833
30 % 6 16 1777

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