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 34319
95 % 1 2 24815 Flexibility: Low
Max RMSD: 0.6, Avg RMSD: 0.6
PDBFlex
90 % 1 2 23973
70 % 71 179 134
50 % 71 179 164
40 % 71 179 178
30 % 71 182 195
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 38 857
95 % 20 43 877 Flexibility: Low
Max RMSD: 2.4, Avg RMSD: 1.2
PDBFlex
90 % 20 43 910
70 % 20 43 937
50 % 20 43 984
40 % 20 43 999
30 % 20 43 996
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 16737
95 % 2 5 10089 Flexibility: Low
Max RMSD: 6.5, Avg RMSD: 2.2
PDBFlex
90 % 420 762 2
70 % 1379 2519 1
50 % 2821 5107 1
40 % 3219 5756 1
30 % 3945 7175 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 16530
95 % 2 5 10064 Flexibility: Low
Max RMSD: 1.4, Avg RMSD: 1.0
PDBFlex
90 % 2 5 9936
70 % 1370 2478 2
50 % 2822 5107 1
40 % 3220 5756 1
30 % 3946 7175 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 1RZ7 1 L Fab 48d light chain 9606
2 3JWD 3 L, O FAB 48D LIGHT CHAIN 9606
3 4DVR 2 L Fab 48d Light chain 9606
4 3JWO 3 L FAB 48D LIGHT CHAIN 9606