Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 4672 |
| PDBID: | 7Q9I |
| Chains: | JK_C |
| Organism: | Severe acute respiratory syndrome coronavirus 2, Homo sapiens |
| Method: | EM |
| Resolution (Å): | 4.90 |
| Reference: | 10.1016/j.chom.2021.11.013 |
| Antibody | |
| Antibody: | Beta-43 Fab |
| Antibody mutation: | No |
| INN (Clinical Trial): | |
| Antigen | |
| Antigen: | SARS-CoV-2 Beta spike glycoprotein |
| Antigen mutation: | Yes |
| Durg Target: | P0DTC2 |
Sequence information
Antibody
Heavy Chain: J
Mutation: NULL
| >7Q9I_J|Chain D[auth E], F[auth H], H[auth J]|Beta-43 heavy chain|Homo sapiens (9606) EVQLVESGGGVVQPGRSLRLSCAASGFTFSSYGMHWVRQAPGKGLEWVAVIWYDGSNNFYADSVKGRFTISRDNFKNTLYLQMNSLRAEDTAVYYCARSYCSGGFCFGYYYGLDVWGQGTTVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDK |
Light Chain: K
Mutation: NULL
| >7Q9I_K|Chain E[auth F], G[auth K], I[auth L]|Beta-43 light chain|Homo sapiens (9606) SYELTQPPSVSVAPGKTATITCGGNNIGTKSVHWYQQKPGQAPVLVIYYNSDRPSGIPERFSGSNSGNTVTLTISRVEAGDEADYYCQVWDSGSDHYVFGTGTKVTVVGQPKANPTVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSYLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPTECS |
Antigen
Chain: C
Mutation: L18F/D80A/D215G/A243I/Q414N/N481K/Q498Y/L611G/S698V
| >7Q9I_C|Chain A, B, C|Spike glycoprotein|Severe acute respiratory syndrome coronavirus 2 (2697049) MFVFLVLLPLVSSQCVNFTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFANPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRGLPQGFSALEPLVDLPIGINITRFQTLHISYLTPGDSSSGWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKSFTVEKGIYQTSNFRVQPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGNIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVKGFNCYFPLQSYGFQPTYGVGYQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFNFNGLTGTGVLTESNKKFLPFQQFGRDIADTTDAVRDPQTLEILDITPCSFGGVSVITPGTNTSNQVAVLYQGVNCTEVPVAIHADQLTPTWRVYSTGSNVFQTRAGCLIGAEHVNNSYECDIPIGAGICASYQTQTNSPGSASSVASQSIIAYTMSLGVENSVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLNRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKDFGGFNFSQILPDPSKPSKRSFIEDLLFNKVTLADAGFIKQYGDCLGDIAARDLICAQKFNGLTVLPPLLTDEMIAQYTSALLAGTITSGWTFGAGAALQIPFAMQMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTASALGKLQDVVNQNAQALNTLVKQLSSNFGAISSVLNDILSRLDPPEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDPLQPELDSFKEELDKYFKNHTSPDVDLGDISGINASVVNIQKEIDRLNEVAKNLNESLIDLQELGKYEQGSGYIPEAPRDGQAYVRKDGEWVLLSTFLGRSLEVLFQGPGHHHHHHHHGSAWSHPQFEKGGGSGGGSGGSAWSHPQFEK |
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)
| J: TRP52 TYR53 ASP54 SER56 ASN57 ASN58 PHE59 TYR100 SER102 GLY103 GLY104 PHE105 PHE107 TYR109 TYR110 TYR111 K: GLY28 THR29 LYS30 SER31 TYR49 ASN50 SER51 ASP52 SER64 ASN65 SER66 TRP90 SER92 ASP95 C: SER13 GLN14 CYS15 VAL16 ASN17 PHE18 THR19 SER71 GLY75 THR76 ARG78 PHE140 TYR144 TYR145 HIS146 LYS147 ASN148 ASN149 MET153 SER155 GLU156 ARG158 SER244 LEU246 THR247 PRO248 GLY249 |
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)
