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Entry information

Complex
AACDB_ID: 3400
PDBID: 7BEN
Chains: HL_E
Organism: Severe acute respiratory syndrome coronavirus 2, Homo sapiens
Method: XRD
Resolution (Å): 2.50
Reference: 10.1016/j.cell.2021.02.032
Antibody
Antibody: COVOX-253 Fab
Antibody mutation: No
INN (Clinical Trial):
Antigen
Antigen: SARS-CoV-2 Spike glycoprotein RBD
Antigen mutation: Yes
Durg Target: P0DTC2; P0DTC2;

Sequence information

Antibody

Heavy Chain: H
Mutation: NULL

>7BEN_H|Chain B[auth D], G[auth H]|COVOX-253 heavy chain|Homo sapiens (9606)
QVQLVQSGPEVKKPGTSVKVSCKASGFTFTTSAVQWVRQARGQRLEWIGWIVVGSGNTNYAQKFQERVTITRDMSTTTAYMELSSLRSEDTAVYFCAAPHCNSTSCYDAFDIWGQGTMVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDK

Light Chain: L
Mutation: NULL

>7BEN_L|Chain C[auth F], H[auth L]|COVOX-253 light chain|Homo sapiens (9606)
DIQMTQSPGTLSLSPGEGATLSCRASQSVSSSYLAWYQQKPGQAPRLLIYGASSGATGIPDRFSGSGSGTDFTLTISRLEPEDFAVYYCQQYGSSPYTFGQGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Antigen

Chain: E
Mutation: P204K

>7BEN_E|Chain A[auth C], F[auth E]|Spike glycoprotein|Severe acute respiratory syndrome coronavirus 2 (2697049)
ETGHHHHHHTNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGKK

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: THR30 THR31 SER32 ALA33 TRP50 VAL52 GLY54 SER55 ASN57 MET74 PRO99 SER103 THR104 SER105 CYS106 TYR107 ASP108 ALA109 PHE110

L: SER32 TYR33 TYR92 GLY93 TYR97

E: LYS417 TYR421 TYR453 LEU455 PHE456 ARG457 LYS458 TYR473 GLN474 ALA475 GLY476 SER477 THR478 PRO479 GLY485 PHE486 ASN487 CYS488 TYR489 GLN493

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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