Sequence Similarity Clusters for the Entities in PDB 3JWD

Entity #1 | Chains: A,B
HIV-1 GP120 ENVELOPE GLYCOPROTEIN protein, length: 379 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name Structural variation in cluster
100 % 1 1 36099
95 % 1 2 26065 Flexibility: Low
Max RMSD: 0.6, Avg RMSD: 0.5
PDBFlex
90 % 1 2 25131
70 % 72 192 130
50 % 72 192 157
40 % 72 192 168
30 % 72 195 184
Entity #2 | Chains: C,D
T-cell surface glycoprotein CD4 protein, length: 184 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name Structural variation in cluster
100 % 19 40 854
95 % 20 46 804 Flexibility: Low
Max RMSD: 2.4, Avg RMSD: 1.2
PDBFlex
90 % 20 46 836
70 % 20 46 887
50 % 20 46 935
40 % 20 46 960
30 % 20 46 943
Entity #3 | Chains: L,O
FAB 48D LIGHT CHAIN protein, length: 213 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name Structural variation in cluster
100 % 2 4 17700
95 % 2 5 10673 Flexibility: Low
Max RMSD: 1.5, Avg RMSD: 0.9
PDBFlex
90 % 461 844 2
70 % 1461 2696 1
50 % 2995 5473 1
40 % 3410 6175 1
30 % 4161 7653 1
Entity #4 | Chains: H,P
FAB 48D HEAVY CHAIN protein, length: 220 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name Structural variation in cluster
100 % 2 4 17481
95 % 2 5 10646 Flexibility: Low
Max RMSD: 1.6, Avg RMSD: 1.1
PDBFlex
90 % 2 5 10500
70 % 1453 2655 2
50 % 2996 5473 1
40 % 3411 6175 1
30 % 4162 7653 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 1RZ7 2 H Fab 48d heavy chain 9606
2 3JWD 4 H, P FAB 48D HEAVY CHAIN 9606
3 4DVR 3 H Fab 48d Heavy chain 9606
4 3JWO 4 H FAB 48D Heavy CHAIN 9606
5 3J70 1 A, M, R monoclonal antibody 17b light chain 9606