Sequence Similarity Clusters for the Entities in PDB 4LAJ

Entity #1 | Chains: A,B,F,J
HIV-1 YU2 gp120 envelope glycoprotein protein, length: 376 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name Structural variation in cluster
100 % 5 8 4535
95 % 5 8 5339 Flexibility: Low
Max RMSD: 1.1, Avg RMSD: 0.7
PDBFlex
90 % 5 8 5385
70 % 26 101 323
50 % 26 101 381
40 % 26 101 399
30 % 26 102 409
Entity #2 | Chains: C,D,G,K
CD4-mimetic miniprotein M48U1 protein, length: 28 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name Structural variation in cluster
100 % 4 10 2711
95 % 5 14 2366 Flexibility: No
Max RMSD: 2.4, Avg RMSD: 0.5
PDBFlex
90 % 5 14 2444
70 % 5 16 2135
50 % 5 16 2170
40 % 5 16 2213
30 % 5 16 2216
Entity #3 | Chains: H,I,L,M
Llama single domain antibody, JM4 protein, length: 129 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name Structural variation in cluster
100 % 1 1 24437
95 % 1 1 23816 Flexibility: No
Max RMSD: 0.3, Avg RMSD: 0.3
PDBFlex
90 % 1 1 18488
70 % 189 497 8
50 % 263 744 6
40 % 263 757 6
30 % 394 1135 6

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 4JZZ 1 A HIV-1 YU2 gp120 glycoprotein 11676
2 4JZW 1 A, G HIV-1 YU2 gp120 glycoprotein 11676
3 4KA2 1 A HIV-1 YU2 gp120 11676
4 4K0A 1 A HIV-1 YU2 gp120 glycoprotein 11676
5 4LAJ 1 A, B, F, J HIV-1 YU2 gp120 envelope glycoprotein 11676
6 4RWY 1 A HIV-1 YU2 gp120 11676
7 4R4F 1 A HIV-1 Env gp120 11676
8 3TGQ 1 A, B, C, D HIV-1 YU2 gp120 11676