Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 3374 |
| PDBID: | 7B27 |
| Chains: | D_B |
| Organism: | Severe acute respiratory syndrome coronavirus 2, Vicugna pacos |
| Method: | XRD |
| Resolution (Å): | 2.90 |
| Reference: | 10.15252/embr.202052325 |
| Antibody | |
| Antibody: | NM1230 Nanobody |
| Antibody mutation: | No |
| INN (Clinical Trial): | |
| Antigen | |
| Antigen: | SARS-CoV-2 Spike glycoprotein RBD |
| Antigen mutation: | No |
| Durg Target: | P0DTC2 |
Sequence information
Antibody
Chain: D
Mutation: NULL
| >7B27_D|Chain C[auth CCC], D[auth DDD]|neutralizing nanobody NM1230|Vicugna pacos (30538) QVQLVESGGGLVRPGGSLRLSCVGSGFTFSGYAMNWYRQAPGKALELVAGISNAGDLTHYEEPMKGRVAISRANDKNTVYLQMDDLKPEDTAVYRCHAPGVRVGTGERKDVWGQGAQVTVSSEQKLISEEDLKKKHHHHHH |
Antigen
Chain: B
Mutation: NULL
| >7B27_B|Chain A[auth AAA], B[auth aba]|Surface glycoprotein|Severe acute respiratory syndrome coronavirus 2 (2697049) RVQPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVN |
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)
| D: VAL2 GLN3 LEU4 ALA33 ASN35 TYR37 GLN39 GLY42 LYS43 ALA44 LEU45 LEU47 HIS59 GLU61 ARG95 HIS97 PRO99 ARG102 GLU107 ARG108 ASP110 TRP112 GLY113 GLN114 B: ARG28 SER31 TYR33 ALA34 LYS99 LYS126 TYR131 ASN132 LEU134 TYR135 LEU137 PHE138 ARG148 ILE150 SER151 THR152 GLY164 VAL165 GLU166 GLY167 TYR171 PHE172 LEU174 GLN175 SER176 |
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)
