Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 3581 |
| PDBID: | 7DCC |
| Chains: | DH_E |
| Organism: | Mus musculus, Severe acute respiratory syndrome coronavirus 2 |
| Method: | EM |
| Resolution (Å): | 4.30 |
| Reference: | 10.1038/s41467-020-20465-w |
| Antibody | |
| Antibody: | 3C1 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: D
Mutation: NULL
| >7DCC_D|Chain A, B, C[auth D]|The heavy chain of 3C1 fab|Mus musculus (10090) EVQLQESGPSLVKPSQTLSLTCSVTGDSITNGYWNWIRKFPGNKLEYMGYISYSGSTYYSPSLKSRISITRDTSKNQHYLQLNSVTSEDTATYYCASDYHGSKYYFDYWGQGTTLTVSSAKTTPPSVYPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSTWPSETVTCNVAHPASSTKVDKKIVPRDCG |
Light Chain: H
Mutation: NULL
| >7DCC_H|Chain E[auth F], F[auth H], I[auth M]|The light chain of 3C1 fab|Mus musculus (10090) DIVMTQSHKFMSTSVGHRVSITCKASQDVGNDVAWYQQKPGQSPKLLIYWASTRHTGVPDRFTGSGSGTDFTLTISNVQSEDLADYFCQQYNRYPYTFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC |
Antigen
Chain: E
Mutation: R682G/R683S/R685S/K986P/V987P
| >7DCC_E|Chain D[auth E], G[auth I], H[auth K]|Spike glycoprotein|Severe acute respiratory syndrome coronavirus 2 (2697049) MFVFLVLLPLVSSQCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGDSSSGWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKSFTVEKGIYQTSNFRVQPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFNFNGLTGTGVLTESNKKFLPFQQFGRDIADTTDAVRDPQTLEILDITPCSFGGVSVITPGTNTSNQVAVLYQDVNCTEVPVAIHADQLTPTWRVYSTGSNVFQTRAGCLIGAEHVNNSYECDIPIGAGICASYQTQTNSPGSASSVASQSIIAYTMSLGAENSVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLNRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKDFGGFNFSQILPDPSKPSKRSFIEDLLFNKVTLADAGFIKQYGDCLGDIAARDLICAQKFNGLTVLPPLLTDEMIAQYTSALLAGTITSGWTFGAGAALQIPFAMQMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTASALGKLQDVVNQNAQALNTLVKQLSSNFGAISSVLNDILSRLDPPEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDPLQPELDSFKEELDKYFKNHTSPDVDLGDISGINASVVNIQKEIDRLNEVAKNLNESLIDLQELGKYEQGSGYIPEAPRDGQAYVRKDGEWVLLSTFLENLYFQGDYKDDDDKHHHHHHHHH |
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: ASN31 TYR33 TYR50 SER52 TYR53 SER54 SER56 TYR58 TYR59 SER60 PRO61 LYS64 ASP98 HIS100 H: ASP1 ILE2 SER26 GLN27 ASP28 VAL29 GLY30 ASN31 ASP32 SER67 GLY68 THR69 PHE71 GLN90 ASN92 ARG93 TYR94 PRO95 E: LEU368 TYR369 ASN370 ALA372 PHE374 SER375 THR376 PHE377 LYS378 CYS379 TYR380 GLY381 VAL382 SER383 PRO384 THR385 LYS386 ARG403 ASP405 GLU406 VAL407 ARG408 GLN409 ILE410 ALA411 PRO412 GLY413 GLN414 THR415 GLY416 LYS417 VAL433 GLY502 VAL503 GLY504 TYR505 |
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)
