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 36912
95 % 1 2 26619 Flexibility: No
Max RMSD: 0.4, Avg RMSD: 0.4
PDBFlex
90 % 1 2 25670
70 % 73 207 127
50 % 73 207 147
40 % 73 207 161
30 % 73 210 177
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 40 873
95 % 20 46 828 Flexibility: Low
Max RMSD: 2.4, Avg RMSD: 1.2
PDBFlex
90 % 20 46 859
70 % 20 46 909
50 % 20 46 953
40 % 20 46 983
30 % 20 46 963
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 18077
95 % 100 214 68 Flexibility: Low
Max RMSD: 1.5, Avg RMSD: 0.9
PDBFlex
90 % 469 865 2
70 % 1484 2765 1
50 % 3053 5625 1
40 % 3484 6382 1
30 % 4269 7934 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 17862
95 % 2 5 10881 Flexibility: Low
Max RMSD: 1.6, Avg RMSD: 1.1
PDBFlex
90 % 2 5 10719
70 % 1480 2728 2
50 % 3054 5625 1
40 % 3485 6382 1
30 % 4270 7934 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