Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 4659 |
| PDBID: | 7Q3R |
| Chains: | F_A |
| Organism: | Severe acute respiratory syndrome coronavirus 2, Vicugna pacos |
| Method: | XRD |
| Resolution (Å): | 1.92 |
| Reference: | Not available or To be published |
| Antibody | |
| Antibody: | F04 VHH |
| 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: F
Mutation: NULL
| >7Q3R_F|Chain B[auth F]|VHH-F04|Vicugna pacos (30538) AMAEVQLVESGGGLVQAGGSLRLSCAASGRAFSRYFMGWFRQAPGKEREFVAGISRSGGSTDYANFVKGRFTISRDNAKNTVYLQMNSLKPEDTAVYYCAATVDYSGTLTAARGREDYDDWGQGIQVTVSSAAAHHHHHHHH |
Antigen
Chain: A
Mutation: NULL
| >7Q3R_A|Chain A|Spike glycoprotein|Severe acute respiratory syndrome coronavirus 2 (2697049) NITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSFLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPK |
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)
| F: GLU44 SER57 THR58 ASP59 TYR60 ASN62 THR99 VAL100 TYR102 SER103 THR105 LEU106 THR107 ALA108 ALA109 ARG110 GLY111 ARG112 GLU113 ASP114 ASP116 A: TYR369 ASN370 SER373 PHE374 SER375 THR376 PHE377 LYS378 CYS379 TYR380 GLY381 VAL382 SER383 PRO384 THR385 GLY404 ARG408 PRO412 GLY413 GLN414 ASP427 ASP428 PHE429 VAL503 TYR508 |
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)
