Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 6366 |
| PDBID: | 8HEB |
| Chains: | ED_A |
| Organism: | Severe acute respiratory syndrome coronavirus 2, Oryctolagus cuniculus |
| Method: | EM |
| Resolution (Å): | 3.53 |
| Reference: | 10.1016/j.bbrc.2023.04.002 |
| Antibody | |
| Antibody: | RmAb 9H1 Fab |
| Antibody mutation: | No |
| INN (Clinical Trial): | |
| Antigen | |
| Antigen: | SARS-CoV-2 spike glycoprotein |
| Antigen mutation: | Yes |
| Durg Target: | P0DTC2 |
Sequence information
Antibody
Heavy Chain: E
Mutation: NULL
| >8HEB_E|Chain E, G, I|rabbit antibody 9H1 heavy chain|Oryctolagus cuniculus (9986) QSVEESGGRLVTPGTPLTLTCTVSGFSLSRYAMSWVRQAPGKGLEWIGIIVDSGHTAYASWAKGRFTISRTSTTVDLKMTSLTTEDTATYFCARETGGGAFYVFEFWGPGTVVTVSS |
Light Chain: D
Mutation: NULL
| >8HEB_D|Chain D, F, H|rabbit antibody 9H1 light chain|Oryctolagus cuniculus (9986) QVLTQTPSSVSAAVGGTVTINCQASEDIYDNLVWYQQKPGQPPKLLIYDASTLAFGVSSRFRGSGSGTHFTLTMRDVQCDDAATYYCQGEFSCSSGDCTAFGGGTEVVVK |
Antigen
Chain: A
Mutation: R682G/R683S/R685S/K986P/V987P
| >8HEB_A|Chain A, B, C|Spike glycoprotein|Severe acute respiratory syndrome coronavirus 2 (2697049) MFVFLVLLPLVSSQCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGDSSSGWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKSFTVEKGIYQTSNFRVQPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFNFNGLTGTGVLTESNKKFLPFQQFGRDIADTTDAVRDPQTLEILDITPCSFGGVSVITPGTNTSNQVAVLYQDVNCTEVPVAIHADQLTPTWRVYSTGSNVFQTRAGCLIGAEHVNNSYECDIPIGAGICASYQTQTNSPGSASSVASQSIIAYTMSLGAENSVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLNRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKDFGGFNFSQILPDPSKPSKRSFIEDLLFNKVTLADAGFIKQYGDCLGDIAARDLICAQKFNGLTVLPPLLTDEMIAQYTSALLAGTITSGWTFGAGAALQIPFAMQMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTASALGKLQDVVNQNAQALNTLVKQLSSNFGAISSVLNDILSRLDPPEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDPLQPELDSFKEELDKYFKNHTSPDVDLGDISGINASVVNIQKEIDRLNEVAKNLNESLIDLQELGKYEQ |
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)
| D: ASP27 ILE28 TYR29 ASP30 ASN31 GLU90 SER92 CYS93 SER94 CYS98 E: ILE49 VAL51 HIS55 THR56 ALA57 GLY98 GLY99 ALA100 PHE101 TYR102 A: ARG403 ASP405 GLU406 ARG408 GLN409 VAL445 TYR449 SER494 GLY496 GLN498 PRO499 THR500 ASN501 GLY502 VAL503 GLY504 TYR505 GLN506 |
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)
