Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 5524 |
| PDBID: | 7X2L |
| Chains: | B_E |
| Organism: | Severe acute respiratory syndrome coronavirus 2, Vicugna pacos |
| Method: | XRD |
| Resolution (Å): | 2.40 |
| Reference: | 10.1038/s41467-022-35642-2 |
| Antibody | |
| Antibody: | 3-2A2-4 VHH |
| Antibody mutation: | No |
| INN (Clinical Trial): | |
| Antigen | |
| Antigen: | SARS-CoV-2 spike glycoprotein RBD |
| Antigen mutation: | No |
| Durg Target: | P0DTC2 |
Sequence information
Antibody
Chain: B
Mutation: NULL
| >7X2L_B|Chain B|Nanobody 3-2A2-4|Vicugna pacos (30538) QVQLQESGGGLVQPGESLRLSCAASGSISTLNVMGWYRQAPGKQRELVAQITLDGSPEYADSVKGRFTITKDGAQSTLYLQMNNLKPEDTAVYFCKLENGGFFYYWGQGTQVTVSTHHHHHH |
Antigen
Chain: E
Mutation: NULL
| >7X2L_E|Chain A[auth E]|Spike protein S1|Severe acute respiratory syndrome coronavirus 2 (2697049) TNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPK |
Interaction
1、Solvent accessible surface areas (SASA) were calculated (Naccess V2.1.1) for each residue in antibody and antigen, respectively. The residues with SASA loss in binding of more than 1Å2 were classified as interacting residues.
Interacting residues (ΔSASA based)
| B: GLN1 SER27 SER29 THR30 LEU31 ASN32 VAL33 THR52 LEU53 ASP54 GLU98 ASN99 GLY100 GLY101 PHE102 PHE103 TYR104 E: THR333 ASN334 LEU335 CYS336 PHE338 GLY339 GLU340 PHE342 ASN343 VAL362 ALA363 ASP364 TYR365 VAL367 LEU368 ASN370 SER371 SER373 PHE374 PRO527 |
2、We defined interacting paratope-epitope residues by a distance cutoff of < 5Å . Two amino acids are considered as interacting residues if they have at least one atom within a distance of 5 Å from any atom.
Interacting residues (Atom distance based)
