Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 5656 |
| PDBID: | 7Y7K |
| Chains: | BC_A |
| Organism: | Severe acute respiratory syndrome coronavirus 2, Homo sapiens |
| Method: | EM |
| Resolution (Å): | 4.40 |
| Reference: | 10.1093/procel/pwac042 |
| Antibody | |
| Antibody: | 1F 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: B
Mutation: NULL
| >7Y7K_B|Chain B|1F VH|Homo sapiens (9606) EVQLVESGPGLVKPSETLSLTCTVSGGSISSSSYYWGWIRQPPGKGLEWIGSIYYRGSTYYNPSLKSRVTISVDTSKNQFSLKLSSVTAADTAVYYCARHVRSAYYYGSGSYRDEGNWFDPWGQGTLVTVSS |
Light Chain: C
Mutation: NULL
| >7Y7K_C|Chain C|1F VL|Homo sapiens (9606) QSVLTQPPSVSGAPGQRVTISCTGTRSNIGAGHDVHWYQQLPGTAPKLLIYGNNNRPSGVPDRFSGAKSGTSASLAITGLQAEDEADYYCQSYDRTLTSYVFGTGTKVTVL |
Antigen
Chain: A
Mutation: NULL
| >7Y7K_A|Chain A|Spike protein S1|Severe acute respiratory syndrome coronavirus 2 (2697049) CPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLS |
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)
| Chain residues position delta_SASA
: residuesposition B: SER32 SER33 TYR35 TYR55 ARG56 TYR60 ARG102 SER103 TYR106 TYR107 GLY110 SER111 TYR112 ASP114 C: HIS33 ARG95 A: LYS417 LEU455 PHE456 GLN474 ALA475 GLY476 SER477 VAL483 GLU484 PHE486 ASN487 TYR489 PRO491 LEU492 GLN493 |
2、We defined interacting paratope-epitope residues by a distance cutoff of < 6 Å . Two amino acids are considered as interacting residues if they have at least one atom within a distance of 6 Å from any atom.
Interacting residues (Atom distance based)
