Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 5525 |
| PDBID: | 7X2M |
| Chains: | B_E |
| Organism: | Severe acute respiratory syndrome coronavirus 2, Vicugna pacos |
| Method: | XRD |
| Resolution (Å): | 1.80 |
| Reference: | 10.1038/s41467-022-35642-2 |
| Antibody | |
| Antibody: | 1-2C7 VHH |
| Antibody mutation: | No |
| INN (Clinical Trial): | |
| Antigen | |
| Antigen: | SARS-CoV-2 spike glycoprotein RBD |
| Antigen mutation: | Yes |
| Durg Target: | P0DTC2 |
Sequence information
Antibody
Chain: B
Mutation: NULL
| >7X2M_B|Chain B|1-2C7|Vicugna pacos (30538) QVQLQESGGGLVQPGGSLRLSCAASGDTLDLYAIGWFRQTPGEEREGVSCISPSGSRTNYADSVKGRFTISRDNAKNTVYLQMNGLRPEDTAVYFCAGSRPSAHYCSHYPTEYDDWGQGTQVTV |
Antigen
Chain: E
Mutation: K85N/E152K/N169Y
| >7X2M_E|Chain A[auth E]|Spike protein S1|Severe acute respiratory syndrome coronavirus 2 (2697049) TNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGNIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVKGFNCYFPLQSYGFQPTYGVGYQPYRVVVLSFELLHAPATVCGPKKHHHHHH |
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)
| Chain residues position delta_SASA
: residuesposition B: GLN1 LEU31 PRO53 ARG57 SER99 ARG100 PRO101 SER102 ALA103 HIS104 TYR105 TYR109 THR111 GLU112 ASP114 E: TYR369 ASN370 SER371 ALA372 SER373 PHE374 SER375 THR376 PHE377 LYS378 CYS379 TYR380 SER383 PRO384 THR385 GLY404 ASP405 ARG408 ASN437 VAL503 GLY504 TYR508 |
2、We defined interacting paratope-epitope residues by a distance cutoff of < 6 Å . Two amino acids are considered as interacting residues if they have at least one atom within a distance of 6 Å from any atom.
Interacting residues (Atom distance based)
