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 34871
95 % 1 2 22340 Flexibility: Low
Max RMSD: 0.6, Avg RMSD: 0.6
PDBFlex
90 % 1 2 21687
70 % 69 129 184
50 % 69 129 226
40 % 69 129 245
30 % 69 132 251
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 38 728
95 % 20 43 877 Flexibility: Low
Max RMSD: 2.4, Avg RMSD: 1.2
PDBFlex
90 % 20 43 908
70 % 20 43 936
50 % 20 43 971
40 % 20 43 998
30 % 20 43 979
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 15747
95 % 83 192 62 Flexibility: Low
Max RMSD: 6.5, Avg RMSD: 2.2
PDBFlex
90 % 421 763 2
70 % 1332 2426 1
50 % 2722 4913 1
40 % 2722 4913 1
30 % 3115 5780 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 15683
95 % 2 5 9472 Flexibility: Low
Max RMSD: 1.4, Avg RMSD: 1.0
PDBFlex
90 % 2 5 9373
70 % 1320 2376 2
50 % 2723 4913 1
40 % 2723 4913 1
30 % 3116 5780 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 3JWD 1 A, B HIV-1 GP120 ENVELOPE GLYCOPROTEIN 11676
2 3JWO 1 A HIV-1 GP120 ENVELOPE GLYCOPROTEIN 9606