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 35653
95 % 1 2 25743 Flexibility: Low
Max RMSD: 0.6, Avg RMSD: 0.5
PDBFlex
90 % 1 2 24833
70 % 71 188 128
50 % 71 188 156
40 % 71 188 169
30 % 71 191 181
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 39 839
95 % 20 45 812 Flexibility: Low
Max RMSD: 2.4, Avg RMSD: 1.2
PDBFlex
90 % 20 45 842
70 % 20 45 884
50 % 20 45 933
40 % 20 45 958
30 % 20 45 942
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 17455
95 % 2 5 10495 Flexibility: Low
Max RMSD: 1.5, Avg RMSD: 0.9
PDBFlex
90 % 447 819 2
70 % 1435 2637 1
50 % 2950 5362 1
40 % 3360 6051 1
30 % 4107 7514 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 17244
95 % 2 5 10471 Flexibility: Low
Max RMSD: 1.6, Avg RMSD: 1.1
PDBFlex
90 % 2 5 10333
70 % 1431 2600 2
50 % 2951 5362 1
40 % 3361 6051 1
30 % 4108 7514 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