Sequence Similarity Clusters for the Entities in PDB 4I3R

Entity #1 | Chains: G
Outer domain of HIV-1 gp120 (KER2018 OD4.2.2) protein, length: 190 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name Structural variation in cluster
100 % 1 2 43584
95 % 1 2 36602 Flexibility: Low
Max RMSD: 1.7, Avg RMSD: 1.7
PDBFlex
90 % 1 2 34921
70 % 1 2 31015
50 % 1 2 26480
40 % 1 2 23255
30 % 1 2 19387
Entity #2 | Chains: H
Heavy chain of VRC-PG04 Fab protein, length: 228 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name Structural variation in cluster
100 % 2 5 8818
95 % 2 5 8864 Flexibility: Low
Max RMSD: 1.5, Avg RMSD: 1.2
PDBFlex
90 % 2 5 8770
70 % 1754 2706 2
50 % 3627 5577 1
40 % 4125 6322 1
30 % 5125 7862 1
Entity #3 | Chains: L
Light chain of VRC-PG04 Fab protein, length: 208 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name Structural variation in cluster
100 % 2 5 8817
95 % 2 5 8863 Flexibility: Low
Max RMSD: 1.0, Avg RMSD: 0.8
PDBFlex
90 % 2 5 8769
70 % 1783 2747 1
50 % 3628 5577 1
40 % 4126 6322 1
30 % 5126 7862 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


ACTION - (A) Select for download / view details OR (B) Select two chains for comparison
Rank PDB ID Entity ID Chains Description Details Taxonomy EC Number
1 3SE9 3 L Light chain of antibody VRC-PG04 antibody light chain 9606
2 4I3R 3 L Light chain of VRC-PG04 Fab 9606
3 4I3S 3 L Light chain of VRC-PG04 Fab 9606
4 6CRQ 4 E, K, L PGV04 VL 9606
5 3J5M 3 C, G, K PGV04 light chain Fab 9606