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 14408
95 % 10 15 3911 Flexibility: Medium
Max RMSD: 16.1, Avg RMSD: 5.5
PDBFlex
90 % 10 15 3946
70 % 58 126 179
50 % 58 126 219
40 % 58 126 240
30 % 58 129 246
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 38 685
95 % 16 43 824 Flexibility: Low
Max RMSD: 2.4, Avg RMSD: 1.1
PDBFlex
90 % 16 43 852
70 % 16 43 888
50 % 16 43 929
40 % 16 43 952
30 % 16 43 927
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 1247
95 % 12 25 1367 Flexibility: Low
Max RMSD: 3.5, Avg RMSD: 0.7
PDBFlex
90 % 321 683 3
70 % 891 1841 2
50 % 2209 4537 1
40 % 2209 4537 1
30 % 2522 5342 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 1245
95 % 12 25 1365 Flexibility: Low
Max RMSD: 2.3, Avg RMSD: 0.8
PDBFlex
90 % 12 25 1386
70 % 1073 2197 1
50 % 2210 4537 1
40 % 2210 4537 1
30 % 2523 5342 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.