Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 6258 |
| PDBID: | 8GJN |
| Chains: | AB_C |
| Organism: | Mus musculus, Severe acute respiratory syndrome coronavirus 2 |
| Method: | EM |
| Resolution (Å): | 3.60 |
| Reference: | 10.1002/jmv.28673 |
| Antibody | |
| Antibody: | 17B10 Fab |
| Antibody mutation: | No |
| INN (Clinical Trial): | |
| Antigen | |
| Antigen: | SARS-CoV-2 B.1.3 (G614) spike glycoprotein RBD |
| Antigen mutation: | No |
| Durg Target: | P0DTC2 |
Sequence information
Antibody
Heavy Chain: A
Mutation: NULL
| >8GJN_A|Chain A|Heavy chain of 17B10 Fab|Mus musculus (10090) MGWSWIFLFLLSGTAGVLSEVQLQQSGPELVKPGASVRISCKTSGYTFTEYSMFWVKQSHGQSLEWIGGINPNDDSTTYKQNFKGKATLTVDKSSSTAFMELRSLTSEDSAVYYCTRDRYDGRVVDFWGQGTTLTVSS |
Light Chain: B
Mutation: NULL
| >8GJN_B|Chain B|Light chain of 17B10 Fab|Mus musculus (10090) MRVPAHVFGFLLLWFPGTRCDIQMTQSPSSLSASLGERVSLICRASQEISGYLSWLQQKPDGTIKRLIYAASTLDSGVPKRFSGSRSGSEYSLTISSPESEDFADYYCLQYASYPWTFGGGTKLEIK |
Antigen
Chain: C
Mutation: NULL
| >8GJN_C|Chain C|Spike protein S2'|Severe acute respiratory syndrome coronavirus 2 (2697049) TNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPKKS |
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)
| A: SER52 PHE54 GLY69 ASN71 ASN73 ASP74 SER76 THR77 THR78 ASP118 ARG119 TYR120 VAL124 B: SER50 TYR52 TYR111 ALA112 SER113 TYR114 TRP116 C: LEU455 PHE456 LYS458 TYR473 GLN474 ALA475 GLY476 SER477 THR478 PRO479 ASN481 PHE486 ASN487 TYR489 |
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)
