Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 4982 |
| PDBID: | 7T5O |
| Chains: | HL_C |
| Organism: | Severe acute respiratory syndrome-related coronavirus, Homo sapiens |
| Method: | EM |
| Resolution (Å): | 3.39 |
| Reference: | 10.1038/s41467-023-36295-5 |
| Antibody | |
| Antibody: | GAR03 Fab |
| Antibody mutation: | No |
| INN (Clinical Trial): | |
| Antigen | |
| Antigen: | SARS-CoV-2 D614G VFLIP spike glycoprotein trimer |
| Antigen mutation: | No |
| Durg Target: | P0DTC2 |
Sequence information
Antibody
Heavy Chain: H
Mutation: NULL
| >7T5O_H|Chain D[auth H]|GAR03 Fab heavy chain|Homo sapiens (9606) QVQLVQSGAEVKKPGASVKVSCKASGYTFSSYDINWVRQAPGQGLEWMGWMSPNSGNTGYAQKFQGRVTMTRSTSMSTAYMELSSLRSEDTAVYFCARMSSSLTNYLDYWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCGSHHHHHH |
Light Chain: L
Mutation: NULL
| >7T5O_L|Chain E[auth L]|GAR03 Fab light chain|Homo sapiens (9606) SYVLTQPPSVAVAPGQTARIRCGENDIGSKNVHWYQQKSGQAPVLVVYDDSDRPSGIPERFSGSNSGNTATLTISRVEAGDEADYYCQVWDSTGDHPDVVFGGGTKLTVLGQPKAAPSVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSYLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPTEC |
Antigen
Chain: C
Mutation: NULL
| >7T5O_C|Chain A, B, C|Spike glycoprotein|Severe acute respiratory syndrome-related coronavirus (694009) QCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGDSSSGWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKSFTVEKGIYQTSNFRVQPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFNFNGLTGTGVLTESNKKFLPFQQFGRDIADTTDAVRDPQTLEILDITPCSFGGVSVITPGTNTSNQVAVLYQGVNCTEVPVAIHADQLTPTWRVYSTGSNVFQTRAGCLIGAEHVNNSYECDIPIGAGICASYQGGSGGSSIIAYTMSLGAENSVACSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLNRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKDFGGFNFSQILPDPSKPSKRSPIEDLLFNKVTLADAGFIKQYGDCLGDIAARDLICAQKFNGLTVLPPLLTDEMIAQYTSALLAGTICSGWTFGAGPALQIPFPMQMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTPSALGKLQDVVNQNAQALNTLVKQLSSNFGAISSVLNDILSRLDKPEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDPLQPELDSFKEELDKYFKNHTSPDVDLGDISGINASVVNIQKEIDRLNEVAKNLNESLIDLQELGKYEQYIKGSGYIPEAPRDGQAYVRKDGEWVLLSTFLLEVLFQGPAGWSHPQFEKGGGSGGGSGGGSWSHPQFEK |
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)
| H: TRP50 ASN57 LEU103 THR104 ASN105 L: SER1 TYR2 ASP26 GLY28 SER29 LYS30 ASN31 ASP49 ASP50 SER51 ASP52 GLU59 ASN65 GLY67 ASN68 TRP90 ASP91 SER92 THR93 GLY94 ASP95 PRO97 C: PRO337 GLU340 VAL341 ALA344 THR345 ARG346 ALA348 SER349 TYR351 ALA352 TRP353 ASN354 ARG355 LYS356 ARG357 SER359 ASN450 TYR451 LEU452 PHE464 GLU465 ARG466 ILE468 SER469 GLU471 LEU582 |
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)
