Sequence Similarity Clusters for the Entities in PDB 5W4L

Entity #1 | Chains: A,G
clade A/E 93TH057 HIV-1 gp120 core protein, length: 385 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name Structural variation in cluster
100 % 20 24 1240
95 % 55 68 615 Flexibility: Low
Max RMSD: 1.9, Avg RMSD: 0.8
PDBFlex
90 % 55 68 642
70 % 82 110 325
50 % 82 110 384
40 % 82 110 408
30 % 83 112 418
Entity #2 | Chains: M,N
CD4 mimetic peptide M48U1 protein, length: 28 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name Structural variation in cluster
100 % 6 12 2326
95 % 9 16 2234 Flexibility: No
Max RMSD: 2.4, Avg RMSD: 0.5
PDBFlex
90 % 9 16 2300
70 % 11 18 1991
50 % 11 18 2118
40 % 11 18 2170
30 % 11 18 2116
Entity #3 | Chains: F,H
Antibody N5-i5 Fab heavy chain protein, length: 226 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name Structural variation in cluster
100 % 3 3 13526
95 % 3 3 12960 Flexibility: Medium
Max RMSD: 8.9, Avg RMSD: 4.5
PDBFlex
90 % 271 347 16
70 % 2305 3058 1
50 % 4829 6427 1
40 % 4830 6428 1
30 % 4865 6475 1
Entity #4 | Chains: I,L
Antibody N5-i5 light chain protein, length: 217 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name Structural variation in cluster
100 % 3 3 12930
95 % 6 9 4626 Flexibility: Medium
Max RMSD: 9.1, Avg RMSD: 4.8
PDBFlex
90 % 71 97 266
70 % 447 656 8
50 % 4830 6427 1
40 % 4831 6428 1
30 % 4866 6475 1
Entity #5 | Chains: B,D
Antibody N12-i3 Fab heavy chain protein, length: 225 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name Structural variation in cluster
100 % 1 1 41934
95 % 1 1 34684 Flexibility: Low
Max RMSD: 0.8, Avg RMSD: 0.8
PDBFlex
90 % 1 1 34758
70 % 2306 3058 1
50 % 4831 6427 1
40 % 4832 6428 1
30 % 4867 6475 1
Entity #6 | Chains: C,E
Antibody N12-i3 light chain protein, length: 215 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name Structural variation in cluster
100 % 1 1 41933
95 % 94 114 232 Flexibility: Low
Max RMSD: 6.2, Avg RMSD: 1.8
PDBFlex
90 % 197 252 71
70 % 1916 2488 2
50 % 4832 6427 1
40 % 4833 6428 1
30 % 4868 6475 1

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