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Entry information

Complex
AACDB_ID: 4646
PDBID: 7PS5
Chains: HL_E
Organism: Homo sapiens, Severe acute respiratory syndrome coronavirus 2
Method: XRD
Resolution (Å): 3.14
Reference: 10.1016/j.chom.2021.11.013
Antibody
Antibody: Beta-47 Fab
Antibody mutation: No
INN (Clinical Trial):
Antigen
Antigen: SARS-CoV-2 Beta variant spike glycoprotein RBD
Antigen mutation: Yes
Durg Target: P0DTC2

Sequence information

Antibody

Heavy Chain: H
Mutation: NULL

>7PS5_H|Chain A[auth H]|Beta-47 Fab heavy chain|Homo sapiens (9606)
QVQLVESGPEMKKPGTSVKVSCKASGFTFITSAVQWVRQARGQRLEWMGWIAVGSGNTNYAQKFQDRVTINRDMSTSTAYMELSSLRSEDTAVYYCAAPHCNRTSCHDGFDIWGQGTMVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDK

Light Chain: L
Mutation: NULL

>7PS5_L|Chain B[auth L]|Beta-47 Fab light chain|Homo sapiens (9606)
EIVLTQSPGTLSLSPGERATLSCRASQSVSRNYLAWYQQKPGQVPRLLIYGASSRATGIPDRFRGSGSGTDFTLTINRLESEDFAVYYCQQYGSSLFTFGPGTKVDIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Antigen

Chain: E
Mutation: K99N/E166K/N183Y

>7PS5_E|Chain C[auth E]|Spike protein S1|Severe acute respiratory syndrome coronavirus 2 (2697049)
MGCVAETGHHHHHHTNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGNIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVKGFNCYFPLQSYGFQPTYGVGYQPYRVVVLSFELLHAPATVCGKK

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)

H: ILE30 THR31 SER32 ALA33 TRP50 ALA52 GLY54 SER55 ASN57 ASP73 MET74 SER75 PRO99 ARG103 THR104 SER105 CYS106 HIS107 ASP108 GLY109 PHE110

L: SER30 ARG31 ASN32 TYR33 GLY51 TYR92 GLY93 SER95 PHE97

E: THR415 ASN417 ASP420 TYR421 TYR453 LEU455 PHE456 ARG457 LYS458 ASN460 TYR473 ALA475 GLY476 SER477 THR478 PRO479 CYS480 VAL483 LYS484 GLY485 PHE486 ASN487 CYS488 TYR489 PHE490 GLN493 TYR505

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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