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 2955
95 % 4 9 3684 Flexibility: Low
Max RMSD: 1.4, Avg RMSD: 0.9
PDBFlex
90 % 5 12 2802
70 % 75 126 178
50 % 75 126 223
40 % 75 126 242
30 % 75 129 248
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 1274
95 % 18 32 1118 Flexibility: Low
Max RMSD: 4.0, Avg RMSD: 0.9
PDBFlex
90 % 426 701 3
70 % 1401 2287 1
50 % 2848 4633 1
40 % 2848 4633 1
30 % 3306 5461 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 1272
95 % 16 25 1398 Flexibility: Low
Max RMSD: 3.9, Avg RMSD: 1.0
PDBFlex
90 % 16 25 1422
70 % 1378 2244 2
50 % 2849 4633 1
40 % 2849 4633 1
30 % 3307 5461 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 24582
95 % 2 2 20992 Flexibility: Low
Max RMSD: 0.8, Avg RMSD: 0.6
PDBFlex
90 % 2 2 20398
70 % 9 15 1866
50 % 9 15 1888
40 % 9 15 1892
30 % 9 15 1832

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.