Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 6178 |
| PDBID: | 8F0I |
| Chains: | EF_B |
| Organism: | Severe acute respiratory syndrome coronavirus 2, Homo sapiens |
| Method: | XRD |
| Resolution (Å): | 3.70 |
| Reference: | 10.1016/j.isci.2023.108009 |
| Antibody | |
| Antibody: | COVA309-22 Fab |
| Antibody mutation: | No |
| INN (Clinical Trial): | |
| Antigen | |
| Antigen: | SARS-CoV-2 spike glycoprotein RBD |
| Antigen mutation: | No |
| Durg Target: | P0DTC2 |
Sequence information
Antibody
Heavy Chain: E
Mutation: NULL
| >8F0I_E|Chain B[auth C], E, H|COVA309-22 heavy chain|Homo sapiens (9606) EVQLVESGGGVVQPGRSLRLSCAASGFTFSSYGMHWVRQAPGKGLEWVAVIWYDGSNKHYADSVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCARDEGTMTTYFDYWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSC |
Light Chain: F
Mutation: NULL
| >8F0I_F|Chain C[auth D], F, I|COVA309-22 light chain|Homo sapiens (9606) EIVLTQSPSSLSASVGDRVTITCRASQSISSYLNWYQQKPGKAPKLLIYDASSLQSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCQQSYSTPPWTFGQGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGECS |
Antigen
Chain: B
Mutation: NULL
| >8F0I_B|Chain A, D[auth B], G|Spike protein S1|Severe acute respiratory syndrome coronavirus 2 (2697049) TNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPKKSGHHHHHH |
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)
| E: SER31 TYR32 GLY33 VAL50 TRP52 TYR53 SER56 ASN57 LYS58 HIS59 TYR60 LYS65 ASP99 GLU100 GLY101 THR102 MET103 THR104 THR105 F: GLU1 GLN27 SER28 TYR32 SER91 TYR92 SER93 THR94 PRO95 TRP97 B: TYR365 SER366 TYR369 SER371 ALA372 SER373 PHE374 SER375 PHE377 LYS378 CYS379 TYR380 GLY381 VAL382 SER383 PRO384 THR385 LYS386 LEU387 ASN388 ASP389 LEU390 PHE392 PRO412 GLN414 ASP427 PHE429 THR430 LEU517 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)
