Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 3046 |
| PDBID: | 6VO3 |
| Chains: | GJ_C |
| Organism: | Homo sapiens, Human immunodeficiency virus 1 |
| Method: | EM |
| Resolution (Å): | 4.25 |
| Reference: | 10.1128/JVI.01214-20 |
| Antibody | |
| Antibody: | PGV04 Fab |
| Antibody mutation: | No |
| INN (Clinical Trial): | |
| Antigen | |
| Antigen: | HIV-1 AMC009 SOSIP.v4.2 gp120 |
| Antigen mutation: | No |
| Durg Target: | |
Sequence information
Antibody
Heavy Chain: G
Mutation: NULL
| >6VO3_G|Chain A[auth G], E[auth H], I|PGV04 heavy chain|Homo sapiens (9606) QVQLVQSGSGVKKPGASVRVSCWTSEDIFERTELIHWVRQAPGQGLEWIGWVKTVTGAVNFGSPDFRQRVSLTRDRDLFTAHMDIRGLTQGDTATYFCARQKFYTGGQGWYFDLWGRGTLIVVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSC |
Light Chain: J
Mutation: NULL
| >6VO3_J|Chain B[auth J], F[auth K], J[auth L]|PGV04 light chain|Homo sapiens (9606) EIVLTQSPGTLSLSPGETASLSCTAASYGHMTWYQKKPGQPPKLLIFATSKRASGIPDRFSGSQFGKQYTLTITRMEPEDFARYYCQQLEFFGQGTRLEIRRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC |
Antigen
Chain: C
Mutation: NULL
| >6VO3_C|Chain C[auth A], G[auth C], K[auth D]|AMC009 SOSIP.v4.2 envelope glycoprotein gp120|Human immunodeficiency virus 1 (11676) ARADKLWVTVYYGVPVWKEATTTLFCASDAKAYDTEVRNVWATHACVPTDPNPQEVVLENVTENFNMWKNDMVEQMHEDIISLWDQSLKPCVKLTPLCVTLNCTDYVGNATNASTTNATGGIGGTVERGEIKNCSFNITTSIRDKVQKEYALFYKLDIVPIDNDNTNNSYRLINCNTSVIKQACPKVSFEPIPIHYCAPAGFAILKCNDKKFNGTGPCTNVSTVQCTHGIRPVVSTQLLLNGSLAEKEVVIRSQNFTNNAKVIIVQLNESVVINCTRPNNNTRKSIHIAPGRWFYTTGAIIGDIRQAHCNISRVKWNNTLKQIATKLREQFKNKTIAFNQSSGGDPEIVMHSFNCGGEFFYCNTTQLFNSTWNDTEVSNYNDITHITLPCRIKQIINMWQKVGKAMYAPPIRGQIRCSSNITGLLLTRDGGSNENKTSETETFRPAGGDMRDNWRSELYKYKVVKIEPLGVAPTKCKRRVVQ |
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)
| G: GLU30 LEU34 LEU45 GLU46 TRP47 TRP50 VAL52 THR53 GLY54 ALA55 VAL56 ASN57 PHE58 GLY59 SER60 ARG64 THR70 ARG71 ARG73 ASP74 TYR98 THR99 J: GLU1 ILE2 LEU4 SER27 LEU91 GLU96 PHE97 PHE98 C: THR198 GLN275 ASN276 THR278 ASN279 ASN280 ALA281 LYS282 LYS357 SER365 GLY366 GLY367 ASP368 ILE371 GLN428 VAL430 GLY431 THR455 ARG456 ASP457 GLY458 GLY459 SER460 ASN461 GLU462 THR467 ARG469 ALA471 GLY472 GLY473 ASP474 |
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)
