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 14876
95 % 10 15 4030 Flexibility: Medium
Max RMSD: 16.1, Avg RMSD: 6.3
PDBFlex
90 % 10 15 4067
70 % 58 127 179
50 % 58 127 224
40 % 58 127 244
30 % 58 130 249
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 38 709
95 % 16 43 842 Flexibility: Low
Max RMSD: 2.4, Avg RMSD: 1.2
PDBFlex
90 % 16 43 874
70 % 16 43 908
50 % 16 43 956
40 % 16 43 982
30 % 16 43 955
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 1295
95 % 14 32 1127 Flexibility: Low
Max RMSD: 3.5, Avg RMSD: 0.8
PDBFlex
90 % 339 720 3
70 % 1116 2327 1
50 % 2283 4713 1
40 % 2283 4713 1
30 % 2611 5567 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 1293
95 % 12 25 1408 Flexibility: Low
Max RMSD: 3.9, Avg RMSD: 1.0
PDBFlex
90 % 12 25 1433
70 % 1107 2280 2
50 % 2284 4713 1
40 % 2284 4713 1
30 % 2612 5567 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.