Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 5799 |
| PDBID: | 7ZRC |
| Chains: | JK_A |
| Organism: | Severe acute respiratory syndrome coronavirus 2, Tequatrovirus T4, Homo sapiens |
| Method: | EM |
| Resolution (Å): | 3.50 |
| Reference: | 10.1016/j.cell.2022.05.014 |
| Antibody | |
| Antibody: | Omi-38 Fab |
| Antibody mutation: | No |
| INN (Clinical Trial): | |
| Antigen | |
| Antigen: | SARS-CoV-2 Beta spike glycoprotein ECD |
| Antigen mutation: | Yes |
| Durg Target: | P0DTC2 |
Sequence information
Antibody
Heavy Chain: J
Mutation: NULL
| >7ZRC_J|Chain D[auth F], F[auth H], H[auth J]|Omi-38 Fab Heavy Chain|Homo sapiens (9606) QVQLVESGAEVKKPGSSVKVSCKASGGNFNMYTISWVRQAPGRGLEWMGRFIPIANKANYAQNFPGRVTITADKSTSTVYMELRSLTSDDTAVYYCARSGSYDAFDVWGQGTMVTVSS |
Light Chain: K
Mutation: NULL
| >7ZRC_K|Chain E[auth G], G[auth K], I[auth L]|Omi-38 Fab Light Chain|Homo sapiens (9606) AIRMTQSPSTLSASVGDRVTITCRASQTINSWLAWYQQKPGKAPKLLIYDASNLESGVPSRFSGSGSGTEFTLTISSLQPDDFATYYCQQYESYSPITFGQGTRLEIK |
Antigen
Chain: A
Mutation: L18F/D80A/D215G/A243I/Q414N/N481K/Q498Y/L611G/N679G/S680S/R682S/S698V/R983P/L984P/F1229L
| >7ZRC_A|Chain A, B, C|Spike glycoprotein,Fibritin|Severe acute respiratory syndrome coronavirus 2 (2697049) MFVFLVLLPLVSSQCVNFTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFANPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRGLPQGFSALEPLVDLPIGINITRFQTLHISYLTPGDSSSGWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKSFTVEKGIYQTSNFRVQPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGNIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVKGFNCYFPLQSYGFQPTYGVGYQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFNFNGLTGTGVLTESNKKFLPFQQFGRDIADTTDAVRDPQTLEILDITPCSFGGVSVITPGTNTSNQVAVLYQGVNCTEVPVAIHADQLTPTWRVYSTGSNVFQTRAGCLIGAEHVNNSYECDIPIGAGICASYQTQTNSPGSASSVASQSIIAYTMSLGVENSVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLNRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKDFGGFNFSQILPDPSKPSKRSFIEDLLFNKVTLADAGFIKQYGDCLGDIAARDLICAQKFNGLTVLPPLLTDEMIAQYTSALLAGTITSGWTFGAGAALQIPFAMQMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTASALGKLQDVVNQNAQALNTLVKQLSSNFGAISSVLNDILSRLDPPEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDPLQPELDSFKEELDKYFKNHTSPDVDLGDISGINASVVNIQKEIDRLNEVAKNLNESLIDLQELGKYEQGSGYIPEAPRDGQAYVRKDGEWVLLSTFLGRSLEVLFQGPGHHHHHHHHGSAWSHPQFEKGGGSGGGSGGSAWSHPQFEK |
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)
| J: ASN28 ASN30 MET31 THR33 ARG50 ILE52 PRO53 ILE54 ALA55 LYS57 ASN59 LYS74 SER75 SER101 TYR102 ASP103 K: ASN30 SER31 TRP32 ASP50 SER52 ASN53 TYR91 GLU92 SER93 TYR94 SER95 A: THR342 ARG343 TYR348 ASN437 LEU438 ASP439 SER440 LYS441 VAL442 GLY443 GLY444 ASN445 TYR446 ASN447 TYR448 LEU449 THR467 ILE469 VAL480 LYS481 PHE487 LEU489 GLN490 SER491 |
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)
