Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 5650 |
| PDBID: | 7Y0W |
| Chains: | HL_R |
| Organism: | Homo sapiens |
| Method: | EM |
| Resolution (Å): | 3.42 |
| Reference: | 10.1016/j.celrep.2022.111845 |
| Antibody | |
| Antibody: | BD55-5840 Fab |
| Antibody mutation: | No |
| INN (Clinical Trial): | |
| Antigen | |
| Antigen: | SARS-CoV-2 BA.1 spike glycoprotein RBD |
| Antigen mutation: | No |
| Durg Target: | P0DTC2; P0DTC2; |
Sequence information
Antibody
Heavy Chain: H
Mutation: NULL
| >7Y0W_H|Chain C[auth H]|BD55-5840H|Homo sapiens (9606) VQLAQSGSELRKPGASVKVSCDTSGHSFTSNAIHWVRQAPGQGLEWMGWINTDTGTPTYAQGFTGRFVFSLDTSARTAYLQISSLKADDTAVFYCARERDYSDYFFDYWGQGTLVTVSS |
Light Chain: L
Mutation: NULL
| >7Y0W_L|Chain D[auth L]|BD55-5840L|Homo sapiens (9606) EVVMTQSPASLSVSPGERATLSCRARASLGISTDLAWYQQRPGQAPRLLIYGASTRATGIPARFSGSGSGTEFTLTISSLQSEDSAVYYCQQYSNWPLTFGGGTKVEIK |
Antigen
Chain: R
Mutation: NULL
| >7Y0W_R|Chain E[auth R]|Spike protein S1|Homo sapiens (9606) LCPFDEVFNATRFASVYAWNRKRISNCVADYSVLYNLAPFFTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGNIADYNYKLPDDFTGCVIAWNSNKLDSKVSGNYNYLYRLFRKSNLKPFERDISTEIYQAGNKPCNGVAGFNCYFPLRSYSFRPTYGVGHQPYRVVVLSFELLHAPATVCGK |
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 SER31 ASN32 TRP50 ASN52 ASP54 THR55 THR57 PRO58 THR59 TYR102 SER103 ASP104 TYR105 PHE106 L: GLU1 VAL2 ARG26 ALA27 SER28 LEU29 ASP34 TYR93 SER94 ASN95 TRP96 PRO97 LEU98 R: PRO337 ASP339 GLU340 VAL341 ASN343 ALA344 THR345 ARG346 LYS356 ARG357 ILE358 LYS440 LEU441 ASP442 SER443 LYS444 VAL445 ASN448 ASN450 TYR451 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)
