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 42087
95 % 1 2 35383 Flexibility: Low
Max RMSD: 1.7, Avg RMSD: 1.7
PDBFlex
90 % 1 2 33785
70 % 1 2 30077
50 % 1 2 25662
40 % 1 2 22528
30 % 1 2 18800
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 8478
95 % 2 5 8518 Flexibility: Low
Max RMSD: 1.5, Avg RMSD: 1.2
PDBFlex
90 % 2 5 8449
70 % 1689 2580 2
50 % 3496 5323 1
40 % 3965 6003 1
30 % 4914 7460 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 8477
95 % 2 5 8517 Flexibility: Low
Max RMSD: 1.0, Avg RMSD: 0.8
PDBFlex
90 % 2 5 8448
70 % 1718 2621 1
50 % 3497 5323 1
40 % 3966 6003 1
30 % 4915 7460 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