Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 3361 |
| PDBID: | 7AKD |
| Chains: | DE_C |
| Organism: | Severe acute respiratory syndrome coronavirus 2, Homo sapiens |
| Method: | EM |
| Resolution (Å): | 4.00 |
| Reference: | 10.1126/sciadv.abf5632 |
| Antibody | |
| Antibody: | 47D11 Fv |
| Antibody mutation: | No |
| INN (Clinical Trial): | |
| Antigen | |
| Antigen: | SARS-CoV-2 Spike glycoprotein |
| Antigen mutation: | No |
| Durg Target: | P0DTC2 |
Sequence information
Antibody
Heavy Chain: D
Mutation: NULL
| >7AKD_D|Chain D, F[auth H]|47D11 neutralizing antibody heavy chain|Homo sapiens (9606) QVQLQESGPGLVKPSETLSLTCSVSGGSISSHYWSWIRQPPGKGLEWIGYIYYSGSTNHNPSLKSRVTISVDTSKNQFSLKLSSVTAADTAVYYCARGVLLWFGEPIFEIWGQGTMVTVSS |
Light Chain: E
Mutation: NULL
| >7AKD_E|Chain E, G[auth L]|47D11 neutralizing antibody light chain|Homo sapiens (9606) EIVMTQSPATLSVSPGERATLSCRASQSVSSSLAWYQQKPGQAPRLLIYGASTRAPGIPARFSGSGSGTEFTLTISSLQSEDFAVYYCQQYNNWPLTFGGGTKVEI |
Antigen
Chain: C
Mutation: NULL
| >7AKD_C|Chain A, B, C|Spike glycoprotein|Severe acute respiratory syndrome coronavirus 2 (2697049) MFVFLVLLPLVSSQCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGDSSSGWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKSFTVEKGIYQTSNFRVQPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFNFNGLTGTGVLTESNKKFLPFQQFGRDIADTTDAVRDPQTLEILDITPCSFGGVSVITPGTNTSNQVAVLYQDVNCTEVPVAIHADQLTPTWRVYSTGSNVFQTRAGCLIGAEHVNNSYECDIPIGAGICASYQTQTNSPGSASSVASQSIIAYTMSLGAENSVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLNRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKDFGGFNFSQILPDPSKPSKRSFIEDLLFNKVTLADAGFIKQYGDCLGDIAARDLICAQKFNGLTVLPPLLTDEMIAQYTSALLAGTITSGWTFGAGAALQIPFAMQMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTASALGKLQDVVNQNAQALNTLVKQLSSNFGAISSVLNDILSRLDPPEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDPLQPELDSFKEELDKYFKNHTSPDVDLGDISGINASVVNIQKEIDRLNEVAKNLNESLIDLQELGKYEQGSGYIPEAPRDGQAYVRKDGEWVLLSTFLGRSLEVLFQGPGGSAGGSAGWSHPQFEKGGGSGGGGSGGSAWSHPQFEK |
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)
| D: SER31 HIS32 TYR33 TYR53 ARG97 VAL99 LEU100 LEU101 TRP102 PHE103 GLY104 ILE107 GLU109 E: SER31 LEU46 TYR49 THR53 ARG54 ALA55 PRO56 C: ILE332 THR333 ASN334 LEU335 CYS336 PRO337 PHE338 GLY339 GLU340 PHE342 ASN343 LYS356 VAL362 ALA363 ASP364 TYR365 VAL367 LEU368 PHE374 PRO527 LYS529 |
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)
