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 34953
95 % 1 2 25217 Flexibility: Low
Max RMSD: 0.6, Avg RMSD: 0.5
PDBFlex
90 % 1 2 24344
70 % 71 183 132
50 % 71 183 161
40 % 71 183 173
30 % 71 186 189
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 38 878
95 % 20 43 896 Flexibility: Low
Max RMSD: 2.4, Avg RMSD: 1.2
PDBFlex
90 % 20 43 931
70 % 20 43 956
50 % 20 43 1001
40 % 20 43 1018
30 % 20 43 1009
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 17024
95 % 2 5 10273 Flexibility: Low
Max RMSD: 7.7, Avg RMSD: 2.3
PDBFlex
90 % 432 791 2
70 % 1414 2591 1
50 % 2898 5256 1
40 % 3305 5925 1
30 % 4049 7378 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 16825
95 % 2 5 10249 Flexibility: Low
Max RMSD: 1.6, Avg RMSD: 1.1
PDBFlex
90 % 2 5 10115
70 % 1405 2547 2
50 % 2899 5256 1
40 % 3306 5925 1
30 % 4050 7378 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