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Entry information

Complex
AACDB_ID: 4809
PDBID: 7S0B
Chains: CD_E
Organism: Homo sapiens, Severe acute respiratory syndrome coronavirus 2
Method: XRD
Resolution (Å): 2.90
Reference: 10.1016/j.celrep.2022.110348
Antibody
Antibody: N-612-056 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: C
Mutation: NULL

>7S0B_C|Chain A, C|N-612-056 Fab Heavy Chain|Homo sapiens (9606)
EVQLVESGGGLVQPGGSLRLSCAASGFTFSSYAMSWVRQAPGKGLEWVSLISGSGGSTYYADSVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCARDLWGSGFFAFDVWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTH

Light Chain: D
Mutation: NULL

>7S0B_D|Chain B, D|N-612-056 Light Chain|Homo sapiens (9606)
DIQMTQSPSSLSASVGDRVTITCQASQDISNYLNWYQQKPGKAPKLLIYDASNLETGVPSRFSGSGSGTDFTFTISSLQPEDIATYYCQQDAGTPLTFGQGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Antigen

Chain: E
Mutation: NULL

>7S0B_E|Chain E, F|Spike protein S1|Severe acute respiratory syndrome coronavirus 2 (2697049)
RVQPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPKKSTNLHHHHHH

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: SER52 SER54 GLY56 SER57 THR58 TYR59 LYS65 LEU100 TRP101 SER103 GLY104 PHE105 PHE106

D: ASP28 SER30 TYR32 TYR49 ASP50 ASN53 GLU55 THR56 ASP91 ALA92 GLY93 THR94 LEU96

E: ARG346 ALA348 TYR351 ALA352 TRP353 ASN354 ARG355 LYS356 ARG357 ASN360 TYR396 ARG457 SER459 LYS462 PHE464 GLU465 ARG466 ASP467 ILE468 SER469 THR470 GLU471

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)

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