Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 5645 |
| PDBID: | 7Y0C |
| Chains: | MN_E |
| Organism: | Homo sapiens, Severe acute respiratory syndrome coronavirus 2 |
| Method: | XRD |
| Resolution (Å): | 2.94 |
| Reference: | 10.1016/j.celrep.2022.111845 |
| Antibody | |
| Antibody: | BD55-1403 Fab |
| Antibody mutation: | No |
| INN (Clinical Trial): | |
| Antigen | |
| Antigen: | SARS-CoV-2 Omicron spike glycoprotein RBD |
| Antigen mutation: | Yes |
| Durg Target: | P0DTC2 |
Sequence information
Antibody
Heavy Chain: M
Mutation: NULL
| >7Y0C_M|Chain B[auth A], E[auth M]|BD55-1403 Fab heavy chain|Homo sapiens (9606) QVQLVQSGAEMKKPGSSVKVSCQASGGTFSTYVISWVRQAPGQGLEWMGGIIPIFNTPHYAQKFQGRVTITADESTSTAYMELSSLTSGDTAVYYCARVSQWELLVYWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEP |
Light Chain: N
Mutation: NULL
| >7Y0C_N|Chain A[auth B], D[auth N]|BD55-1403 Fab light chain|Homo sapiens (9606) EIVLTQSPGTLSLSPGERATLSCRASQSINSNYLAWYQQKPGQAPRLLIYGASSRATGIPDRFSGSGSGTDFTLTISRLEPEDFAVYYCQQYGVSPRWTFGQGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRG |
Antigen
Chain: E
Mutation: N2K/G10D/S42L/S44P/S46F/K88N/N111K/G117S/S148N/T149K/E155A/Q164R/G167S/Q169R/N172Y/Y176H
| >7Y0C_E|Chain C[auth E], F[auth R]|Spike protein S1|Severe acute respiratory syndrome coronavirus 2 (2697049) PKITNLCPFDEVFNATRFASVYAWNRKRISNCVADYSVLYNLAPFFTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGNIADYNYKLPDDFTGCVIAWNSNKLDSKVSGNYNYLYRLFRKSNLKPFERDISTEIYQAGNKPCNGVAGFNCYFPLRSYSFRPTYGVGHQPYRVVVLSFELLHAPATVCGPK |
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)
| N: ASN30 ASN32 TYR33 TYR50 GLY51 SER53 SER54 VAL94 M: THR28 SER30 THR31 VAL33 ILE52 ILE54 PHE55 THR57 VAL99 SER100 GLN101 TRP102 GLU103 LEU104 E: ILE332 THR333 ASN334 LEU335 CYS336 PRO337 PHE338 ASP339 GLU340 PHE342 ASN343 ALA344 THR345 VAL362 ALA363 ASP364 TYR365 SER366 VAL367 LEU368 LEU371 LEU441 LEU513 PRO527 |
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)
