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Entry information

Complex
AACDB_ID: 3677
PDBID: 7E8F
Chains: CB_R
Organism: Severe acute respiratory syndrome coronavirus 2, Homo sapiens
Method: EM
Resolution (Å): 3.18
Reference: 10.1038/s41422-021-00514-9
Antibody
Antibody: BD-368-2 Fab
Antibody mutation: No
INN (Clinical Trial):
Antigen
Antigen: SARS-CoV-2 Spike glycoprotein RBD
Antigen mutation: No
Durg Target: P0DTC2; P0DTC2;

Sequence information

Antibody

Heavy Chain: C
Mutation: NULL

>7E8F_C|Chain D[auth C]|368-2 H|Homo sapiens (9606)
EVQLLESGGGVVQPGGSLRLSCAASGFAFTTYAMNWVRQAPGRGLEWVSAISDGGGSAYYADSVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCAKTRGRGLYDYVWGSKDYWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDK

Light Chain: B
Mutation: NULL

>7E8F_B|Chain E[auth B]|368-2 L|Homo sapiens (9606)
DIVMTQSPLSLPVTPGEPASISCRSSQSLLHSNGYLYLDWYLQKPGQSPQLLIYLGSNRASGVPDRFSGSGSGTDFTLKISRVEAEDVGVYYCMQALQTPGTFGQGTRLEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Antigen

Chain: R
Mutation: NULL

>7E8F_R|Chain H[auth R]|Spike protein S1|Severe acute respiratory syndrome coronavirus 2 (2697049)
RVQPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNF

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: SER25 GLY26 PHE27 ALA28 THR30 THR31 TYR32 ASN74 SER75 ASN77 ARG100 GLY101 ARG102 GLY103 LEU104 TYR105 ASP106

B: ASN33 GLY34 TYR35 TYR37 TYR54 LEU55 ASN58

R: ARG346 LYS444 GLY446 TYR449 ASN450 LEU452 THR470 ILE472 PRO479 CYS480 ASN481 GLY482 VAL483 GLU484 GLY485 PHE490 LEU492 GLN493 SER494

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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