Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 5853 |
| PDBID: | 8BSF |
| Chains: | HL_A |
| Organism: | Severe acute respiratory syndrome coronavirus 2, Homo sapiens |
| Method: | XRD |
| Resolution (Å): | 2.20 |
| Reference: | 10.1371/journal.pone.0284173 |
| Antibody | |
| Antibody: | 3D2 Fab |
| Antibody mutation: | No |
| INN (Clinical Trial): | |
| Antigen | |
| Antigen: | SARS-CoV-2 spike glycoprotein RBD |
| Antigen mutation: | Yes |
| Durg Target: | P0DTC2 |
Sequence information
Antibody
Heavy Chain: H
Mutation: NULL
| >8BSF_H|Chain B[auth H]|3D2 FAB HEAVY CHAIN|Homo sapiens (9606) EVQLVQSGAEVKKPGDSLKISCKGSGYSFANYWIGWVRQKPGKGLEWMGIIYPGDSDTRYSPSSLGQVSISVDKSISTAYLQWSSLKASDTAMYYCARHPIHGYGSGSLYNPDYWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKT |
Light Chain: L
Mutation: NULL
| >8BSF_L|Chain C[auth L]|3D2 FAB LIGHT CHAIN|Homo sapiens (9606) QSVLTQPPSVSAAPGQKVTISCSGSNSNIGINYVSWYQQLPETAPKLLIYENNQRPSGIPDRFSGSKSGTSATLGITGLQTGDEADYYCGTWDTSLGAYVFGTGTKVTVLGQPKAAPSVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSYLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPTECS |
Antigen
Chain: A
Mutation: K99N/E166K/N183Y
| >8BSF_A|Chain A|Spike protein S1|Severe acute respiratory syndrome coronavirus 2 (2697049) RVQPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGNIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVKGFNCYFPLQSYGFQPTYGVGYQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFSGHHHHHH |
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: ASN31 TRP33 TYR52 ASP55 ASP57 THR58 ARG59 TYR60 PRO62 LEU65 ILE101 GLY103 TYR104 GLY105 SER106 GLY107 SER108 LEU109 TYR110 L: ILE31 ASN32 TRP92 THR94 SER95 LEU96 GLY97 A: PHE342 ASN343 ALA344 THR345 ARG346 SER366 ALA372 SER373 PHE374 TRP436 ASN437 ASN439 ASN440 LEU441 ASP442 SER443 LYS444 VAL445 GLY446 ASN448 ASN450 TYR451 PRO499 THR500 GLN506 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)
