Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 6402 |
| PDBID: | 8ITU |
| Chains: | IH_C |
| Organism: | Severe acute respiratory syndrome coronavirus 2, Oryctolagus cuniculus |
| Method: | EM |
| Resolution (Å): | 3.68 |
| Reference: | 10.1038/s42003-023-04759-5 |
| Antibody | |
| Antibody: | 1H1 Fv |
| Antibody mutation: | No |
| INN (Clinical Trial): | |
| Antigen | |
| Antigen: | SARS-CoV-2 Omicron BA.1 spike glycoprotein |
| Antigen mutation: | Yes |
| Durg Target: | P0DTC2 |
Sequence information
Antibody
Heavy Chain: I
Mutation: NULL
| >8ITU_I|Chain E, G, I|1H1 heavy chain|Oryctolagus cuniculus (9986) QSLEESGGDLVKPGASLTLTCTASGFSFSSGYDMCWVRQAPGKGLEWIACIGTGSSGNIYYASWAKGRFTISKTSSTTVTLQMTSLTAADTATYFCARDDADYAGPDYFNLWGPGTLVTVSS |
Light Chain: H
Mutation: NULL
| >8ITU_H|Chain D, F, H|1H1 light chain|Oryctolagus cuniculus (9986) DIVMTQTPASVSEPVGGTVTIKCQASESISNWLAWYQQKPGQPPKLLIYAAFTLASGVPSRFKGSGSGTQFTLTINGVECADAATYYCQQTYSSRDVDNVFGGGTEVVVKG |
Antigen
Chain: C
Mutation: A67V/A93I/F140D/H207I/G337D/S369L/S371P/S373F/K415N/N438K/G444W/S475N/T476K/E482A/Q490R/G494S/Q496R/N499Y/Y503H/T545K/D612G/H653Y/N677K/P679H/R680G/R681S/R683S/N762K/D794Y/F815P/N854K/A890P/A897P/A940P/Q952H/N967K/L979F/K984P/V985P
| >8ITU_C|Chain A, B, C|Spike glycoprotein|Severe acute respiratory syndrome coronavirus 2 (2697049) MFVFLVLLPLVSSQCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHVISGTNGTKRFDNPVLPFNDGVYFASIEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLDHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINIVREPEDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGDSSSGWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKSFTVEKGIYQTSNFRVQPTESIVRFPNITNLCPFDEVFNATRFASVYAWNRKRISNCVADYSVLYNLAPFFTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGNIADYNYKLPDDFTGCVIAWNSNKLDSKVSGNYNYLYRLFRKSNLKPFERDISTEIYQAGNKPCNGVAGFNCYFPLRSYSFRPTYGVGHQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFNFNGLKGTGVLTESNKKFLPFQQFGRDIADTTDAVRDPQTLEILDITPCSFGGVSVITPGTNTSNQVAVLYQGVNCTEVPVAIHADQLTPTWRVYSTGSNVFQTRAGCLIGAEYVNNSYECDIPIGAGICASYQTQTKSHGSASSVASQSIIAYTMSLGAENSVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLKRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKYFGGFNFSQILPDPSKPSKRSPIEDLLFNKVTLADAGFIKQYGDCLGDIAARDLICAQKFKGLTVLPPLLTDEMIAQYTSALLAGTITSGWTFGAGPALQIPFPMQMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTPSALGKLQDVVNHNAQALNTLVKQLSSKFGAISSVLNDIFSRLDPPEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDPLQPELDSFKEELDKYFKNHTSPDVDLGDISGINASVVNIQKEIDRLNEVAKNLNESLIDLQELGKYEQGSGYIPEAPRDGQAYVRKDGEWVFLSTFLSGLEVLFQGPGGWSHPQFEKGGGSGGGSGGSAWSHPQFEKGGSHHHHHHHH |
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: SER28 SER30 ASN31 TRP32 TYR49 ALA50 PHE52 THR53 GLY64 SER65 GLY66 SER67 GLY68 THR91 TYR92 SER94 ARG95 I: GLY31 TYR32 TYR60 ASP100 ALA101 ASP102 TYR103 ALA104 GLY105 PRO106 ASP107 TYR108 C: THR345 ARG346 PHE347 ALA348 SER349 TYR351 ALA352 ASN354 LEU441 ASP442 LYS444 VAL445 SER446 ASN448 TYR449 ASN450 TYR451 LEU452 ARG466 ILE468 THR470 PHE490 LEU492 |
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)
