Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 6414 |
| PDBID: | 8J1V |
| Chains: | HK_A |
| Organism: | Severe acute respiratory syndrome coronavirus 2, Homo sapiens |
| Method: | EM |
| Resolution (Å): | 3.01 |
| Reference: | 10.1038/s41467-023-43798-8 |
| Antibody | |
| Antibody: | 8-9D Fab |
| Antibody mutation: | No |
| INN (Clinical Trial): | |
| Antigen | |
| Antigen: | SARS-CoV-2 Omicron BA.5 spike glycoprotein |
| Antigen mutation: | Yes |
| Durg Target: | P0DTC2 |
Sequence information
Antibody
Heavy Chain: H
Mutation: NULL
| >8J1V_H|Chain B[auth C], E[auth F], H|8-9D heavy chain|Homo sapiens (9606) VQLVESGGGLVQPGGSLRLSCAASGLTVSSNYMNWVRQAPGKGLEWVSVFYPGGSTFYADSVRGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCARDHSGHALDIWGQGTMVTVS |
Light Chain: K
Mutation: NULL
| >8J1V_K|Chain C[auth D], F[auth G], I[auth K]|8-9D light chain|Homo sapiens (9606) DIQMTQSPSFLSASVGDRVTITCRASQGISSYLAWYQQKPGKAPKLLIYAASTLQSGVPSRFSGSGSGTEFTLTISSLQPEDFATYYCQHLNSYPSMYTFGQGTKVDI |
Antigen
Chain: A
Mutation: T1/Q2/A3S/F116D/N187G/P313D/Y345F/S347P/S349F/F350A/R379N/E382S/T391N/S414K/N426R/A451N/G452K/G458A/E460V/G472R/P475Y/V479H/Y588G/A629Y/Q653K/N655H/S656G/P657S/R659S/Q738K/I770Y/R791P/A866P/P873P/S916P/V928H/S943K/L960P/D961P
| >8J1V_A|Chain A, D[auth B], G[auth E]|Spike protein S2'|Severe acute respiratory syndrome coronavirus 2 (2697049) TQSYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAISGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLDVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLGRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGDSSSGWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKSFTVEKGIYQTSNFRVQPTESIVRFPNITNLCPFDEVFNATRFASVYAWNRKRISNCVADYSVLYNFAPFFAFKCYGVSPTKLNDLCFTNVYADSFVIRGNEVSQIAPGQTGNIADYNYKLPDDFTGCVIAWNSNKLDSKVGGNYNYRYRLFRKSNLKPFERDISTEIYQAGNKPCNGVAGVNCYFPLQSYGFRPTYGVGHQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFNFNGLTGTGVLTESNKKFLPFQQFGRDIADTTDAVRDPQTLEILDITPCSFGGVSVITPGTNTSNQVAVLYQGVNCTEVPVAIHADQLTPTWRVYSTGSNVFQTRAGCLIGAEYVNNSYECDIPIGAGICASYQTQTKSHGSASSVASQSIIAYTMSLGAENSVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLKRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKYFGGFNFSQILPDPSKPSKRSPIEDLLFNKVTLADAGFIKQYGDCLGDIAARDLICAQKFNGLTVLPPLLTDEMIAQYTSALLAGTITSGWTFGAGPALQIPFPMQMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTPSALGKLQDVVNHNAQALNTLVKQLSSKFGAISSVLNDILSRLDPPEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDPL |
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: VAL3 GLY27 LEU28 THR29 SER31 SER32 ASN33 TYR34 TYR53 PRO54 GLY55 GLY56 SER57 THR58 PHE59 ASN77 ARG98 ASP99 HIS100 SER101 GLY102 K: ILE2 GLN27 GLY28 ILE29 SER30 SER31 TYR32 SER56 SER67 GLY68 THR69 HIS90 LEU91 ASN92 SER93 TYR94 A: ARG403 ASN405 GLU406 GLN409 THR415 GLY416 ASN417 ASP420 TYR421 TYR449 TYR453 LEU455 PHE456 ARG457 LYS458 SER459 ASN460 TYR473 GLN474 ALA475 GLY476 ASN477 LYS478 VAL486 ASN487 TYR489 GLN493 SER494 GLY496 ARG498 THR500 TYR501 GLY502 VAL503 GLY504 HIS505 |
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)
