Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 5296 |
| PDBID: | 7VYR |
| Chains: | HL_R |
| Organism: | Homo sapiens, Severe acute respiratory syndrome coronavirus 2 |
| Method: | XRD |
| Resolution (Å): | 2.20 |
| Reference: | 10.1080/19420862.2021.2021601 |
| Antibody | |
| Antibody: | D27 Fab |
| Antibody mutation: | No |
| INN (Clinical Trial): | |
| Antigen | |
| Antigen: | SARS-CoV-2 spike glycoprotein S1 |
| Antigen mutation: | No |
| Durg Target: | P0DTC2 |
Sequence information
Antibody
Heavy Chain: H
Mutation: NULL
| >7VYR_H|Chain A, D[auth H]|D27 heavy chain|Homo sapiens (9606) MEWSWVFLFFLSVTTGVLSQVQLQQSGAEVKKPGSSVKVSCKASGGTFGNWSISWVRQAPGQGLEWMGGIDPSRGEATYAQKFQGRVTITTDESTSTAYMELSSLRSEDTAVYYCARETEQGGMDVWGQGTTVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTHHHHHHHHH |
Light Chain: L
Mutation: NULL
| >7VYR_L|Chain B, E[auth L]|D27 light chain|Homo sapiens (9606) MGIKMETHSQVFVYMLLWLSGVEGSYELTQPPSVSVAPGKTARITCGGNNIGRKSVHWYQQKPGQAPVLVVYDDSDRPSGIPERFSGSNSGNTATLTISRVEAGDEADYYCQVYDLFSDYVFGTGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC |
Antigen
Chain: R
Mutation: NULL
| >7VYR_R|Chain C, F[auth R]|Spike protein S1|Severe acute respiratory syndrome coronavirus 2 (2697049) MVLVNQSHQGFNKEHTSKMVSAIVLYVLLAAAAHSAFAARVQPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNF |
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 TRP32 SER33 GLY50 ILE51 ASP52 SER54 ARG55 GLU57 THR59 GLU99 THR100 GLU101 GLN102 GLY103 L: GLY28 ARG29 LYS30 TYR90 LEU92 PHE93 ASP95 TYR96 R: TYR369 ASN370 SER371 ALA372 PHE374 SER375 THR376 PHE377 LYS378 TYR380 ARG403 GLY404 ASP405 GLU406 VAL407 ARG408 ALA411 ASN439 ASN440 VAL445 TYR453 TYR495 GLY496 GLN498 PRO499 THR500 ASN501 GLY502 VAL503 GLY504 TYR505 GLN506 TYR508 |
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)
