Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 4779 |
| PDBID: | 7RSO |
| Chains: | IK_D |
| Organism: | Human immunodeficiency virus 1, Homo sapiens |
| Method: | EM |
| Resolution (Å): | 4.10 |
| Reference: | 10.1128/JVI.01552-21 |
| Antibody | |
| Antibody: | PGV04 Fab |
| Antibody mutation: | No |
| INN (Clinical Trial): | |
| Antigen | |
| Antigen: | HIV-1 AMC016 SOSIP.v4.2 gp120 |
| Antigen mutation: | No |
| Durg Target: | |
Sequence information
Antibody
Heavy Chain: I
Mutation: NULL
| >7RSO_I|Chain C[auth G], I[auth H], K[auth I]|PGV04 Fab heavy chain|Homo sapiens (9606) QVQLVQSGSGVKKPGASVRVSCWTSEDIFERTELIHWVRQAPGQGLEWIGWVKTVTGAVNFGSPDFRQRVSLTRDRDLFTAHMDIRGLTQGDTATYFCARQKFYTGGQGWYFDLWGRGTLIVVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCD |
Light Chain: K
Mutation: NULL
| >7RSO_K|Chain D[auth J], J[auth K], L|PGV04 kappa chain|Homo sapiens (9606) EIVLTQSPGTLSLSPGETASLSCTAASYGHMTWYQKKPGQPPKLLIFATSKRASGIPDRFSGSQFGKQYTLTITRMEPEDFARYYCQQLEFFGQGTRLEIRRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC |
Antigen
Chain: D
Mutation: NULL
| >7RSO_D|Chain A, E[auth C], G[auth D]|AMC016 gp120|Human immunodeficiency virus 1 (11676) AEEELWVTVYYGVPVWKEATTTLFCASDAKAYDTEVRNVWATHACVPTDPSPQEVVLANVTENFNMWKNNMVEQMHEDIISLWDQSLKPCVKLTPLCVTLNCTDLGNATDAINRNTTDAPNSTLRTMEEKGEIKNCSFNITTSVRDKMQKEYATFYKLDIVPIDNDNNSYRLINCNTSVITQACPKVSFEPIPIHYCAPAGFAILKCNNKTFNGTGPCTNVSTVQCTHGIRPVVSTQLLLNGSLAEEEIVIRSENFTDNAKTIIVQLNESVEINCTRPNNNTRKSIHIGPGRWFYTTGQIIGNIRQAHCNISRAKWNNTLHKIVKKLREQFRNKTIVFKQSSGGDPEIVMHSFNCGGEFFYCNSTQLFNSTWYGNESSDNPGVEGNITLPCRIKQIINLWQEVGKAMYAPPIGGQIRCSSNITGLLLTRDGGNNNITTEIFRPGGGDMRDNWRSELYKYKVVKIEPLGVAPTKCKRRVVQRRRRRR |
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)
| I: GLU33 LEU34 TRP47 TRP50 VAL52 THR53 GLY54 ALA55 VAL56 ASN57 PHE58 GLY59 SER60 PRO61 ARG64 LEU69 ARG71 ARG73 ASP74 GLN95 PHE97 TYR98 THR99 K: GLU1 VAL3 SER27 LEU91 GLU96 PHE97 D: TRP96 LYS97 THR198 GLU275 ASN276 THR278 ASP279 ASN280 ALA281 LYS282 THR283 ARG354 SER364 SER365 GLY366 GLY367 ASP368 ILE371 GLN428 VAL430 THR455 ARG456 ASP457 GLY458 GLY459 ASN460 ASN461 ASN462 ILE463 ILE467 ARG469 GLY471 GLY472 GLY473 ASP474 ARG476 ASP477 ARG480 |
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)
