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 35017
95 % 1 2 25261 Flexibility: Low
Max RMSD: 0.6, Avg RMSD: 0.5
PDBFlex
90 % 1 2 24388
70 % 71 183 133
50 % 71 183 162
40 % 71 183 174
30 % 71 186 190
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 38 883
95 % 20 43 906 Flexibility: Low
Max RMSD: 2.4, Avg RMSD: 1.2
PDBFlex
90 % 20 43 940
70 % 20 43 963
50 % 20 43 1009
40 % 20 43 1024
30 % 20 43 1013
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 17059
95 % 2 5 10293 Flexibility: Low
Max RMSD: 7.7, Avg RMSD: 2.3
PDBFlex
90 % 433 793 2
70 % 1415 2593 1
50 % 2903 5263 1
40 % 3310 5933 1
30 % 4056 7388 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 16856
95 % 2 5 10267 Flexibility: Low
Max RMSD: 1.6, Avg RMSD: 1.1
PDBFlex
90 % 2 5 10133
70 % 1407 2550 2
50 % 2904 5263 1
40 % 3311 5933 1
30 % 4057 7388 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