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Entry information

Complex
AACDB_ID: 3198
PDBID: 6XDG
Chains: CA_E
Organism: Severe acute respiratory syndrome coronavirus 2, Homo sapiens
Method: EM
Resolution (Å): 3.90
Reference: 10.1126/science.abd0827
Antibody
Antibody: REGN10987 Fab
Antibody mutation: No
INN (Clinical Trial): Masavibart(Approved)
Antigen
Antigen: SARS-CoV-2 Spike glycoprotein RBD
Antigen mutation: No
Durg Target: P0DTC2; P0DTC2;

Sequence information

Antibody

Heavy Chain: C
Mutation: NULL

>6XDG_C|Chain D[auth C]|REGN10987 antibody Fab fragment heavy chain|Homo sapiens (9606)
QVQLVESGGGVVQPGRSLRLSCAASGFTFSNYAMYWVRQAPGKGLEWVAVISYDGSNKYYADSVKGRFTISRDNSKNTLYLQMNSLRTEDTAVYYCASGSDYGDYLLVYWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDK

Light Chain: A
Mutation: NULL

>6XDG_A|Chain E[auth A]|REGN10987 antibody Fab fragment light chain|Homo sapiens (9606)
QSALTQPASVSGSPGQSITISCTGTSSDVGGYNYVSWYQQHPGKAPKLMIYDVSKRPSGVSNRFSGSKSGNTASLTISGLQSEDEADYYCNSLTSISTWVFGGGTKLTVLGQPKAAPSVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSYLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPTECS

Antigen

Chain: E
Mutation: NULL

>6XDG_E|Chain A[auth E]|Spike protein S1|Severe acute respiratory syndrome coronavirus 2 (2697049)
RVQPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFEQKLISEEDLGGEQKLISEEDLHHHHHH

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: ASN31 TYR32 ALA33 TYR35 VAL50 SER52 TYR53 ASP54 SER56 ASN57 TYR59 ASP101 TYR102 GLY103 ASP104 TYR105

A: TYR32 TYR34 LEU93 SER95 TRP99

E: ARG346 ASN439 ASN440 LEU441 SER443 LYS444 VAL445 GLY446 GLY447 ASN448 TYR449 ASN450 GLN498 PRO499 THR500 ASN501

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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