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 35296
95 % 1 2 22633 Flexibility: Low
Max RMSD: 0.6, Avg RMSD: 0.6
PDBFlex
90 % 1 2 21963
70 % 70 130 184
50 % 70 130 225
40 % 70 130 242
30 % 70 133 251
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 % 17 38 733
95 % 20 43 881 Flexibility: Low
Max RMSD: 2.4, Avg RMSD: 1.2
PDBFlex
90 % 20 43 915
70 % 20 43 944
50 % 20 43 976
40 % 20 43 1006
30 % 20 43 990
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 15993
95 % 92 209 56 Flexibility: Low
Max RMSD: 6.5, Avg RMSD: 2.2
PDBFlex
90 % 438 788 2
70 % 1361 2474 1
50 % 2781 5011 1
40 % 2781 5011 1
30 % 3222 5941 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 15930
95 % 2 5 9612 Flexibility: Low
Max RMSD: 1.4, Avg RMSD: 1.0
PDBFlex
90 % 2 5 9512
70 % 1349 2424 2
50 % 2782 5011 1
40 % 2782 5011 1
30 % 3223 5941 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