Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 3607 |
| PDBID: | 7DK4 |
| Chains: | cd_B |
| Organism: | Mus musculus, Severe acute respiratory syndrome coronavirus 2 |
| Method: | EM |
| Resolution (Å): | 3.80 |
| Reference: | 10.1038/s41467-020-20465-w |
| Antibody | |
| Antibody: | 2H2 Fab |
| Antibody mutation: | No |
| INN (Clinical Trial): | |
| Antigen | |
| Antigen: | SARS-CoV-2 Spike glycoprotein |
| Antigen mutation: | No |
| Durg Target: | P0DTC2 |
Sequence information
Antibody
Heavy Chain: c
Mutation: NULL
| >7DK4_c|Chain A[auth a], F[auth c], H[auth e]|The heavy chain of 2H2 Fab|Mus musculus (10090) QVQLKQSGPSLVQPSQSLSITCTVSGFSLTSYGVHWVRQSPGKGLEWLGVMWRGGNTDYNAAFMSRLSITKDNSKSQVFFKMNSLQTDDTAIYYCAKNGGAHAMDFWGQGTSVTVSSAKTTPPSVYPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSTWPSETVTCNVAHPASSTKVDKKI |
Light Chain: d
Mutation: NULL
| >7DK4_d|Chain B[auth b], G[auth d], I[auth f]|The light chain of 2H2 Fab|Mus musculus (10090) NIVLTQSPASLAVSLGQRATISCRASESVDSYGNSFLHWYQQKPGQPPKLLIYLASNLESGVPARFSGSGSRTDFTLTIDPVEADDAATYYCQQNNEDPFTFGSGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC |
Antigen
Chain: B
Mutation: NULL
| >7DK4_B|Chain C[auth A], D[auth B], E[auth C]|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)
| c: GLN1 VAL2 GLY26 SER31 TYR32 TRP52 ARG53 GLY54 GLY55 LYS97 ASN98 GLY99 GLY100 ALA101 HIS102 ASP105 PHE106 d: SER28 SER31 TYR32 ASN34 PHE36 TYR53 LEU54 SER56 ASN57 LEU58 GLU59 SER60 GLY61 VAL62 PRO63 ALA64 PHE66 ASN95 ASN96 GLU97 ASP98 PHE100 B: ARG403 ASP405 LYS417 VAL445 GLY446 GLY447 TYR449 LEU452 TYR453 LEU455 PHE456 LYS458 ILE472 TYR473 GLN474 ALA475 CYS480 GLY482 VAL483 GLU484 GLY485 PHE486 ASN487 CYS488 TYR489 PHE490 LEU492 GLN493 SER494 GLY496 GLN498 ASN501 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)
