Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 6175 |
| PDBID: | 8F0H |
| Chains: | BD_C |
| Organism: | Homo sapiens, Severe acute respiratory syndrome coronavirus 2 |
| Method: | EM |
| Resolution (Å): | 3.18 |
| Reference: | 10.1016/j.celrep.2023.112421 |
| Antibody | |
| Antibody: | 1H2 Fab |
| Antibody mutation: | No |
| INN (Clinical Trial): | |
| Antigen | |
| Antigen: | SARS-CoV-2 spike glycoprotein |
| Antigen mutation: | No |
| Durg Target: | P0DTC2; P0DTC2; |
Sequence information
Antibody
Heavy Chain: B
Mutation: NULL
| >8F0H_B|Chain A[auth B]|Antibody Fab 1H2 heavy chain|Homo sapiens (9606) QVQLQQSGGGLVQPGRSLRLSCAASGFTFDDYAMHWVRQAPGKGLEWVSGITWNSGTIGYADSVKGRFTISRDNAKNSLYLQMRSLRAEDTALYYCAKDSGRKLLWGREDYYMGVWGKGTTVTV |
Light Chain: D
Mutation: NULL
| >8F0H_D|Chain C[auth D]|Antibody Fab 1H2 light chain|Homo sapiens (9606) SYELTQPPSVSVAPGKTARITCGGSNIGSKSVHWYQQKPGQAPVLVIYYDSDRPSGIPERFSGSNSGNTATLTISRVEAGDEADYYCQVWDSSSDHVVFGG |
Antigen
Chain: C
Mutation: NULL
| >8F0H_C|Chain B[auth C]|Spike glycoprotein|Severe acute respiratory syndrome coronavirus 2 (2697049) MGVKVLFALICIAVAEAQCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGDSSSGWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKSFTVEKGIYQTSNFRVQPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFNFNGLTGTGVLTESNKKFLPFQQFGRDIADTTDAVRDPQTLEILDITPCSFGGVSVITPGTNTSNQVAVLYQDVNCTEVPVAIHADQLTPTWRVYSTGSNVFQTRAGCLIGAEHVNNSYECDIPIGAGICASYQTQTNSPGSASSVASQSIIAYTMSLGAENSVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLNRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKDFGGFNFSQILPDPSKPSKRSPIEDLLFNKVTLADAGFIKQYGDCLGDIAARDLICAQKFNGLTVLPPLLTDEMIAQYTSALLAGTITSGWTFGAGPALQIPFPMQMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTPSALGKLQDVVNQNAQALNTLVKQLSSNFGAISSVLNDILSRLDPPEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDPLQPELDSFKEELDKYFKNHTSPDVDLGDISGINASVVNIQKEIDRLNEVAKNLNESLIDLQELGKYEQ |
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)
| B: GLY15 ARG16 SER17 ARG19 THR52 TRP53 ASN54 SER55 GLY56 THR57 ILE58 GLY59 TYR60 LYS65 GLY66 THR69 ILE70 SER71 ARG72 ASP73 ASN74 TYR80 GLN82 ARG84 LYS103 LEU104 LEU105 TRP106 GLY107 GLU109 D: TRP90 SER93 SER94 ASP95 C: GLY339 GLU340 VAL341 ASN343 ALA344 THR345 ARG346 PHE347 ALA348 SER349 TYR351 ALA352 ASN354 LYS356 SER399 LYS444 GLY447 ASN448 TYR449 ASN450 LEU452 ARG466 ILE468 SER469 THR470 ILE472 ASN481 GLY482 VAL483 GLU484 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)
