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Entry information

Complex
AACDB_ID: 5842
PDBID: 8BBO
Chains: HL_R
Organism: Severe acute respiratory syndrome coronavirus 2, Homo sapiens
Method: XRD
Resolution (Å): 2.75
Reference: 10.1016/j.celrep.2023.112271
Antibody
Antibody: BA.2-36 Fab
Antibody mutation: No
INN (Clinical Trial):
Antigen
Antigen: SARS-CoV-2 Delta spike glycoprotein RBD
Antigen mutation: No
Durg Target: P0DTC2

Sequence information

Antibody

Heavy Chain: H
Mutation: NULL

>8BBO_H|Chain B[auth H]|IGH@ protein|Homo sapiens (9606)
QVQLVESGPGRVKPSQTLSLTCTVSGDSINSGINYWNWIRQPAGKELEWIGRIFTSGTTHYNPSLKSRVTISVDRSKNEFSLTLNSVTAADTAVYFCGRGGTDDYVDYWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSCDK

Light Chain: L
Mutation: NULL

>8BBO_L|Chain C[auth L]|Immunoglobulin kappa light chain|Homo sapiens (9606)
AIQMTQSPSTLSASVGDRVTITCRASQDINSWLAWYQQKPGKAPKLLIYDASSLHSGVPTRFSGSGSGTEFTLTISSLQPDDFASYYCQQYKSYRTFGRGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Antigen

Chain: R
Mutation: NULL

>8BBO_R|Chain A[auth R]|Spike glycoprotein|Severe acute respiratory syndrome coronavirus 2 (2697049)
HHHHHHTNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYRYRLFRKSNLKPFERDISTEIYQAGSKPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGKK

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: ASN30 SER31 GLY32 ILE33 TYR35 ARG52 PHE54 THR55 SER56 THR58 HIS60 ARG75 THR102 ASP103 ASP104 TYR105

L: GLN27 ASN30 SER31 TRP32 TYR49 ASP50 SER52 TYR91 LYS92 SER93 TYR94

R: THR345 ARG346 TYR351 ASN440 LEU441 ASP442 SER443 LYS444 VAL445 GLY446 GLY447 ASN448 TYR449 ASN450 TYR451 ARG452 ILE468 THR470 ILE472 GLY482 VAL483 GLU484 PHE490 LEU492 ARG509

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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