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 15534
95 % 10 15 4043 Flexibility: Medium
Max RMSD: 16.1, Avg RMSD: 6.3
PDBFlex
90 % 10 15 4093
70 % 60 179 134
50 % 60 179 164
40 % 60 179 178
30 % 60 182 195
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 % 15 38 857
95 % 16 43 877 Flexibility: Low
Max RMSD: 2.4, Avg RMSD: 1.2
PDBFlex
90 % 16 43 910
70 % 16 43 937
50 % 16 43 984
40 % 16 43 999
30 % 16 43 996
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 1522
95 % 15 34 1082 Flexibility: Low
Max RMSD: 3.5, Avg RMSD: 0.8
PDBFlex
90 % 369 762 2
70 % 1220 2519 1
50 % 2497 5107 1
40 % 2864 5756 1
30 % 3515 7175 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 % 11 24 1314
95 % 12 25 1454 Flexibility: Low
Max RMSD: 3.9, Avg RMSD: 1.0
PDBFlex
90 % 12 25 1481
70 % 1212 2478 2
50 % 2498 5107 1
40 % 2865 5756 1
30 % 3516 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