Sequence Similarity Clusters for the Entities in PDB 2NY5

Entity #1 | Chains: G
ENVELOPE GLYCOPROTEIN GP120 protein, length: 317 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name Structural variation in cluster
100 % 3 4 15233
95 % 10 15 4129 Flexibility: Medium
Max RMSD: 16.1, Avg RMSD: 6.3
PDBFlex
90 % 10 15 4165
70 % 58 129 184
50 % 58 129 226
40 % 58 129 245
30 % 58 132 251
Entity #2 | Chains: C
T-cell surface glycoprotein CD4 protein, length: 184 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name Structural variation in cluster
100 % 13 38 728
95 % 16 43 877 Flexibility: Low
Max RMSD: 2.4, Avg RMSD: 1.2
PDBFlex
90 % 16 43 908
70 % 16 43 936
50 % 16 43 971
40 % 16 43 998
30 % 16 43 979
Entity #3 | Chains: L
ANTIBODY 17B, LIGHT CHAIN protein, length: 214 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name Structural variation in cluster
100 % 12 21 1327
95 % 14 32 1158 Flexibility: Low
Max RMSD: 3.5, Avg RMSD: 0.8
PDBFlex
90 % 367 763 2
70 % 1177 2426 1
50 % 2406 4913 1
40 % 2406 4913 1
30 % 2744 5780 1
Entity #4 | Chains: H
ANTIBODY 17B, HEAVY CHAIN protein, length: 229 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name Structural variation in cluster
100 % 12 21 1325
95 % 12 25 1452 Flexibility: Low
Max RMSD: 3.9, Avg RMSD: 1.0
PDBFlex
90 % 12 25 1480
70 % 1166 2376 2
50 % 2407 4913 1
40 % 2407 4913 1
30 % 2745 5780 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