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 42729
95 % 1 2 35929 Flexibility: Low
Max RMSD: 1.7, Avg RMSD: 1.7
PDBFlex
90 % 1 2 34299
70 % 1 2 30505
50 % 1 2 26044
40 % 1 2 22877
30 % 1 2 19099
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 8629
95 % 2 5 8681 Flexibility: Low
Max RMSD: 1.5, Avg RMSD: 1.2
PDBFlex
90 % 2 5 8604
70 % 1713 2629 2
50 % 3544 5421 1
40 % 4021 6121 1
30 % 4974 7588 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 8628
95 % 2 5 8680 Flexibility: Low
Max RMSD: 1.0, Avg RMSD: 0.8
PDBFlex
90 % 2 5 8603
70 % 1742 2670 1
50 % 3545 5421 1
40 % 4022 6121 1
30 % 4975 7588 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