Sequence Similarity Clusters for the Entities in PDB 2NY1

Entity #1 | Chains: A
ENVELOPE GLYCOPROTEIN GP120 protein, length: 317 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name Structural variation in cluster
100 % 1 1 56301
95 % 5 15 4086 Flexibility: Medium
Max RMSD: 16.1, Avg RMSD: 6.3
PDBFlex
90 % 5 15 4123
70 % 26 129 182
50 % 26 129 223
40 % 26 129 241
30 % 26 132 248
Entity #2 | Chains: B
T-cell surface glycoprotein CD4 protein, length: 184 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name Structural variation in cluster
100 % 6 38 718
95 % 7 43 861 Flexibility: Low
Max RMSD: 2.4, Avg RMSD: 1.2
PDBFlex
90 % 7 43 893
70 % 7 43 921
50 % 7 43 966
40 % 7 43 990
30 % 7 43 967
Entity #3 | Chains: C
ANTIBODY 17B, LIGHT CHAIN protein, length: 214 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name Structural variation in cluster
100 % 5 21 1315
95 % 7 32 1148 Flexibility: Low
Max RMSD: 3.5, Avg RMSD: 0.8
PDBFlex
90 % 184 746 3
70 % 596 2392 1
50 % 1224 4843 1
40 % 1224 4843 1
30 % 1366 5705 1
Entity #4 | Chains: D
ANTIBODY 17B, HEAVY CHAIN protein, length: 229 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name Structural variation in cluster
100 % 5 21 1313
95 % 5 25 1428 Flexibility: Low
Max RMSD: 3.9, Avg RMSD: 1.0
PDBFlex
90 % 5 25 1456
70 % 591 2342 2
50 % 1225 4843 1
40 % 1225 4843 1
30 % 1367 5705 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