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 35337
95 % 1 2 25510 Flexibility: Low
Max RMSD: 0.6, Avg RMSD: 0.5
PDBFlex
90 % 1 2 24620
70 % 71 185 132
50 % 71 185 159
40 % 71 185 171
30 % 71 188 189
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 38 888
95 % 20 43 914 Flexibility: Low
Max RMSD: 2.4, Avg RMSD: 1.2
PDBFlex
90 % 20 43 947
70 % 20 43 974
50 % 20 43 1027
40 % 20 43 1039
30 % 20 43 1025
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 17281
95 % 2 5 10377 Flexibility: Low
Max RMSD: 1.5, Avg RMSD: 0.9
PDBFlex
90 % 444 811 2
70 % 1433 2621 1
50 % 2939 5323 1
40 % 3348 6003 1
30 % 4094 7460 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 17074
95 % 2 5 10352 Flexibility: Low
Max RMSD: 1.6, Avg RMSD: 1.1
PDBFlex
90 % 2 5 10215
70 % 1425 2580 2
50 % 2940 5323 1
40 % 3349 6003 1
30 % 4095 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 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