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 33067
95 % 1 2 21192 Flexibility: Low
Max RMSD: 0.6, Avg RMSD: 0.5
PDBFlex
90 % 1 2 20598
70 % 69 126 179
50 % 69 126 220
40 % 69 126 240
30 % 69 129 246
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 38 686
95 % 20 43 826 Flexibility: Low
Max RMSD: 2.4, Avg RMSD: 1.1
PDBFlex
90 % 20 43 854
70 % 20 43 890
50 % 20 43 931
40 % 20 43 955
30 % 20 43 930
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 14904
95 % 62 161 71 Flexibility: Low
Max RMSD: 6.5, Avg RMSD: 2.3
PDBFlex
90 % 371 685 3
70 % 1018 1845 2
50 % 2509 4545 1
40 % 2509 4545 1
30 % 2874 5350 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 14841
95 % 2 5 9024 Flexibility: Low
Max RMSD: 1.6, Avg RMSD: 1.1
PDBFlex
90 % 2 5 8939
70 % 1219 2201 1
50 % 2510 4545 1
40 % 2510 4545 1
30 % 2875 5350 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.


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