Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 6335 |
| PDBID: | 8H08 |
| Chains: | QR_A |
| Organism: | Severe acute respiratory syndrome coronavirus 2, Homo sapiens |
| Method: | EM |
| Resolution (Å): | 3.20 |
| Reference: | 10.1038/s41467-023-37926-7 |
| Antibody | |
| Antibody: | 6-2C Fab |
| Antibody mutation: | No |
| INN (Clinical Trial): | |
| Antigen | |
| Antigen: | SARS-CoV-2 BA.1 spike glycoprotein |
| Antigen mutation: | Yes |
| Durg Target: | P0DTC2; P0DTC2; |
Sequence information
Antibody
Heavy Chain: Q
Mutation: NULL
| >8H08_Q|Chain F[auth I], J[auth N], N[auth Q]|6-2C H chain|Homo sapiens (9606) QVQLVESGGGVVQPGRSLRLSCASSGFTFSTYHMHWVRQPPGKGLEWVAFISYDGSNYYYSDSVKGRFTISRDNSKNTVYLQMNSLRAEDTALYYCARDSSGWHWGVPFDYWGQGTLVTVSS |
Light Chain: R
Mutation: NULL
| >8H08_R|Chain G[auth K], K[auth O], O[auth R]|6-2C L chain|Homo sapiens (9606) EIVLTQSPSSLSASVQDRVTITCRASQVISNYLAWFQQKPGKAPKLLIYAASNLQSGVPSRFRGSGSGTDFTLTISSLQPEDFATYYCQQYNIYPLTFGGGTKVDIK |
Antigen
Chain: A
Mutation: A67V/A93I/F140D/206I/G336D/S368L/S370P/S372F/K414N/N437K/G443S/S474N/T475K/E481A/Q490R/G493S/Q495R/N498Y/Y502H/T544K/D611G/H652Y/N676K/P678H/R679G/R680S/R682S/N761K/D793Y/N853K/Q951H/N966K/L978F/K983P/V984P
| >8H08_A|Chain A, B, C|Spike glycoprotein|Severe acute respiratory syndrome coronavirus 2 (2697049) MFVFLVLLPLVSSQCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHVISGTNGTKRFDNPVLPFNDGVYFASIEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLDHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPIIVREPEDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGDSSSGWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKSFTVEKGIYQTSNFRVQPTESIVRFPNITNLCPFDEVFNATRFASVYAWNRKRISNCVADYSVLYNLAPFFTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGNIADYNYKLPDDFTGCVIAWNSNKLDSKVSGNYNYLYRLFRKSNLKPFERDISTEIYQAGNKPCNGVAGFNCYFPLRSYSFRPTYGVGHQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFNFNGLKGTGVLTESNKKFLPFQQFGRDIADTTDAVRDPQTLEILDITPCSFGGVSVITPGTNTSNQVAVLYQGVNCTEVPVAIHADQLTPTWRVYSTGSNVFQTRAGCLIGAEYVNNSYECDIPIGAGICASYQTQTKSHGSASSVASQSIIAYTMSLGAENSVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLKRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKYFGGFNFSQILPDPSKPSKRSPIEDLLFNKVTLADAGFIKQYGDCLGDIAARDLICAQKFKGLTVLPPLLTDEMIAQYTSALLAGTITSGWTFGAGPALQIPFPMQMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTPSALGKLQDVVNHNAQALNTLVKQLSSKFGAISSVLNDIFSRLDPPEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDPLQPELDSFKEELDKYFKNHTSPDVDLGDISGINASVVNIQKEIDRLNEVAKNLNESLIDLQELGKYEQYIKWPGSGYIPEAPRDGQAYVRKDGEWVLLSTFLGRSLEVLFQGPGHHHHHHHHSAWSHPQFEKGGGSGGGGSGGSAWSHPQFEKGSDYKDDDDK |
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)
| Q: HIS33 HIS35 PHE50 SER52 TYR53 ASP54 SER56 ASN57 TYR58 TYR59 ASP99 SER101 GLY102 TRP103 HIS104 TRP105 GLY106 PRO108 R: GLN27 VAL28 ILE29 SER30 ASN31 TYR32 TYR49 ALA50 ASN53 TYR91 ASN92 ILE93 TYR94 PRO95 A: PHE342 ASN343 ALA344 THR345 VAL367 LEU368 LEU371 PRO373 PHE374 PHE375 TRP436 ASN437 SER438 ASN439 LYS440 LEU441 SER443 LYS444 VAL445 PRO499 THR500 TYR501 GLY502 VAL503 GLN506 TYR508 ARG509 |
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)
