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Entry information

Complex
AACDB_ID: 5593
PDBID: 7XDA
Chains: DE_A
Organism: Homo sapiens, Severe acute respiratory syndrome coronavirus 2
Method: EM
Resolution (Å): 2.98
Reference: 10.1038/s41421-022-00509-9
Antibody
Antibody: BA7208 Fab
Antibody mutation: No
INN (Clinical Trial):
Antigen
Antigen: SARS-CoV-2 Delta spike glycoprotein RBD
Antigen mutation: Yes
Durg Target: P0DTC2; P0DTC2;

Sequence information

Antibody

Heavy Chain: D
Mutation: NULL

>7XDA_D|Chain D|BA7208 fab|Homo sapiens (9606)
EVQLVQSGAEVKKPGESLKISCKGSGYSFTSYYWIGWVRQMPGKGLEWMGIVYPDDSDTRYSPSFQGQVTISADKSISTAYLQWSSLKASDTAMYYCVRHPGGGDWYFDLWGRGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKT

Light Chain: E
Mutation: NULL

>7XDA_E|Chain E|BA7208 fab|Homo sapiens (9606)
DIQMTQSPSTLSASVGDRVTITCRASQSISSWLAWYQQKPGKAPKLLIYKASSLESGVPSRFSGSGSGTEFTLTITSLQPDDFATYYCQQYDSFSWTFGQGTKLEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Antigen

Chain: A
Mutation: L119R/T145K

>7XDA_A|Chain C[auth A]|Spike glycoprotein|Severe acute respiratory syndrome coronavirus 2 (2697049)
NLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYRYRLFRKSNLKPFERDISTEIYQAGSKPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPK

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)

D: SER28 TYR32 TYR33 TRP34 TYR53 ASP56 ASP58 ARG60 PRO101 GLY102 GLY103 GLY104 ASP105 TRP106

E: TRP32 TYR91 ASP92 SER93 PHE94 TRP96

A: THR327 ARG328 ASN421 ASN422 LEU423 SER425 LYS426 VAL427 ASN430 ASN432 PRO481 THR482

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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