Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 3584 |
| PDBID: | 7DCX |
| Chains: | EH_K |
| Organism: | Mus musculus, Severe acute respiratory syndrome coronavirus 2 |
| Method: | EM |
| Resolution (Å): | 5.90 |
| 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: E
Mutation: NULL
| >7DCX_E|Chain A, B, D[auth E]|The heavy chain of 3C1 fab that binds with the up RBD|Mus musculus (10090) EVQLQESGPSLVKPSQTLSLTCSVTGDSITNGYWNWIRKFPGNKLEYMGYISYSGSTYYSPSLKSRISITRDTSKNQHYLQLNSVTSEDTATYYCASDYHGSKYYFDYWGQGTTLTVSSAKTTPPSVYPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSTWPSETVTCNVAHPASSTKVDKKIVPRDCG |
Light Chain: H
Mutation: NULL
| >7DCX_H|Chain E[auth F], F[auth G], G[auth H]|The light chain of 3C1 fab|Mus musculus (10090) DIVMTQSHKFMSTSVGHRVSITCKASQDVGNDVAWYQQKPGQSPKLLIYWASTRHTGVPDRFTGSGSGTDFTLTISNVQSEDLADYFCQQYNRYPYTFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC |
Antigen
Chain: K
Mutation: R682G/R683S/R685S/K986P/V987P
| >7DCX_K|Chain C, H[auth D], I[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)
| Chain residues position delta_SASA
: residuesposition E: THR30 ASN31 GLY32 TYR33 TYR50 ILE51 SER52 TYR53 SER54 SER56 THR57 TYR58 ASP98 TYR99 HIS100 GLY101 SER102 LYS103 TYR105 H: ASP1 ILE2 GLN27 ASP28 VAL29 GLY30 ASN31 ASP32 TRP50 SER52 GLY66 SER67 GLY68 TYR91 ASN92 ARG93 TYR94 TYR96 K: TYR369 ALA372 SER373 PHE374 SER375 THR376 PHE377 LYS378 CYS379 TYR380 GLY381 VAL382 SER383 PRO384 THR385 LYS386 GLY404 ASP405 VAL407 ARG408 GLN409 PRO412 GLY413 GLN414 THR415 GLY416 LYS417 ASP420 TYR421 LYS424 LEU425 ASP427 ASP428 THR430 LEU455 PHE456 ARG457 LYS458 SER459 ASN460 TYR473 ALA475 VAL503 GLY504 TYR505 |
2、We defined interacting paratope-epitope residues by a distance cutoff of < 6 Å . Two amino acids are considered as interacting residues if they have at least one atom within a distance of 6 Å from any atom.
Interacting residues (Atom distance based)
