Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 5654 |
| PDBID: | 7Y72 |
| Chains: | OP_A |
| Organism: | Homo sapiens |
| Method: | EM |
| Resolution (Å): | 4.03 |
| Reference: | 10.1126/sciadv.ade3470 |
| Antibody | |
| Antibody: | E7 Fab |
| Antibody mutation: | No |
| INN (Clinical Trial): | |
| Antigen | |
| Antigen: | SARS-CoV-2 spike glycoprotein |
| Antigen mutation: | Yes |
| Durg Target: | P0DTC2 |
Sequence information
Antibody
Heavy Chain: O
Mutation: NULL
| >7Y72_O|Chain D[auth O]|Fab E7 heavy chain|Homo sapiens (9606) QVQLQESGPGLVKPSETLSLTCTVSGGFIGPHYWSWVRQPPGKGLEWIGYIYISGSTNYNPSLKSRLTISVDMSKSQFSLTLSSATAADTAVYYCARGGGYLETGPFEYWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPK |
Light Chain: P
Mutation: NULL
| >7Y72_P|Chain C[auth P]|Fab E7 light chain|Homo sapiens (9606) DIVMTQSPLSLPVTPGEPASISCRSSQSLLQNNGYNYLAWYLQKPGQSPQLLIYLSSTRASGVPDRFSGSGSGTDFTLKISRVEAEDVGVYYCMQSLQIPGTFGQGTRLEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC |
Antigen
Chain: A
Mutation: R668A/R670A/F802P/A877P/A884P/A927P/K971P/V972P
| >7Y72_A|Chain A, B[auth C]|Spike glycoprotein|Homo sapiens (9606) VNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGDSSSGWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKSFTVEKGIYQTSNFRVQPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFNFNGLTGTGVLTESNKKFLPFQQFGRDIADTTDAVRDPQTLEILDITPCSFGGVSVITPGTNTSNQVAVLYQDVNCTEVPVAIHADQLTPTWRVYSTGSNVFQTRAGCLIGAEHVNNSYECDIPIGAGICASYQTQTNSPRAAASVASQSIIAYTMSLGAENSVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLNRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKDFGGFNFSQILPDPSKPSKRSPIEDLLFNKVTLADAGFIKQYGDCLGDIAARDLICAQKFNGLTVLPPLLTDEMIAQYTSALLAGTITSGWTFGAGPALQIPFPMQMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTPSALGKLQDVVNQNAQALNTLVKQLSSNFGAISSVLNDILSRLDPPEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDPLQPELDSFKEELDKYFKNHTSPDVDLGDISGINASVVNIQKEIDRLNEVAKNLNESLIDLQELGKYEQYIKWP |
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)
| P: GLN31 ASN32 ASN33 GLY34 TYR35 TYR37 TYR54 LEU55 O: ILE29 GLY30 PRO31 TYR33 TYR50 TYR52 ILE53 SER54 SER56 MET73 SER74 TYR101 LEU102 GLU103 THR104 A: LYS378 TYR380 ARG403 ASP405 ARG408 GLN409 ILE410 ALA411 PRO412 GLY413 GLN414 THR415 GLY416 LYS417 ASP420 TYR421 TYR453 LEU455 PHE456 ARG457 LYS458 SER459 ASN460 TYR473 TYR489 GLN493 |
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)
