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 34257
95 % 1 2 24778 Flexibility: Low
Max RMSD: 0.6, Avg RMSD: 0.6
PDBFlex
90 % 1 2 23937
70 % 70 177 135
50 % 70 177 165
40 % 70 177 179
30 % 70 180 196
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 38 853
95 % 20 43 875 Flexibility: Low
Max RMSD: 2.4, Avg RMSD: 1.2
PDBFlex
90 % 20 43 906
70 % 20 43 935
50 % 20 43 983
40 % 20 43 997
30 % 20 43 994
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 16716
95 % 2 5 10072 Flexibility: Low
Max RMSD: 6.5, Avg RMSD: 2.2
PDBFlex
90 % 419 761 2
70 % 1377 2516 1
50 % 2817 5101 1
40 % 3215 5750 1
30 % 3940 7168 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 16507
95 % 2 5 10047 Flexibility: Low
Max RMSD: 1.4, Avg RMSD: 1.0
PDBFlex
90 % 2 5 9918
70 % 1368 2475 2
50 % 2818 5101 1
40 % 3216 5750 1
30 % 3941 7168 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