Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 7308 |
| PDBID: | 7OAP |
| Chains: | C_B |
| Organism: | Lama glama, Severe acute respiratory syndrome coronavirus 2 |
| Method: | XRD |
| Resolution (Å): | 1.90 |
| Reference: | 10.1038/s41467-021-25480-z |
| Antibody | |
| Antibody: | H3 Nanobody |
| Antibody mutation: | No |
| INN (Clinical Trial): | |
| Antigen | |
| Antigen: | SARS-CoV-2 spike glycoprotein RBD |
| Antigen mutation: | No |
| Durg Target: | P0DTC2; P0DTC2; |
Sequence information
Antibody
Chain: C
Mutation: NULL
| >7OAP_C|Chain C[auth FFF]|H3 nanobody|Lama glama (9844) MAQVQLVESGGGLVKTGGSLRLSCAASGRTFSTYSMGWFRQAPGKEREFVAGMRWTGSSTFYSDSVKGRFTVSRNNAKDTVYLHMNSLKPEDTAVYYCAITTIVRAYYTEYTEADFGSWGQGTQVTVSSKHHHHHH |
Antigen
Chain: B
Mutation: NULL
| >7OAP_B|Chain B[auth EEE]|Spike protein S1|Severe acute respiratory syndrome coronavirus 2 (2697049) NITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPKKSTNKHHHHHH |
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)
| C: ARG54 TRP55 THR56 SER58 SER59 THR60 PHE61 TYR62 LYS67 THR102 ILE103 VAL104 ARG105 ALA106 TYR107 TYR108 GLU110 B: TYR119 LEU122 LEU125 PHE126 THR140 GLU141 ILE142 GLY152 VAL153 GLU154 GLY155 TYR159 PHE160 LEU162 GLN163 SER164 |
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)
