Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 6268 |
| PDBID: | 8GPG |
| Chains: | CD_Y |
| Organism: | Homo sapiens, Human immunodeficiency virus 1 |
| Method: | EM |
| Resolution (Å): | 4.10 |
| Reference: | 10.1038/s41467-023-40321-x |
| Antibody | |
| Antibody: | F6 Fab |
| Antibody mutation: | No |
| INN (Clinical Trial): | |
| Antigen | |
| Antigen: | HIV-1 X18 uncleaved prefusion-optimized (UFO) envelope glycoprotein - gp41 |
| Antigen mutation: | No |
| Durg Target: | |
Sequence information
Antibody
Heavy Chain: C
Mutation: NULL
| >8GPG_C|Chain A, C, E|F6 Fab heavy chain|Homo sapiens (9606) QVQLQQWGTGLLKPSETLSLTCAVYGVSLRGYYWTWIRQSPKKGLEWIGEIDEIGRTKYSQSLRSRATLSIDTSKKQFSLRLTSVTAADMATYYCARWRLMMVDEVTRHGMDVWSQGTMVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTHT |
Light Chain: D
Mutation: NULL
| >8GPG_D|Chain B, D, F|F6 Fab light chain|Homo sapiens (9606) DIVMTQSPLSLSVAPGEAASISCRSTQSLLNRNGDNYLEWYLRRPGRSPQLLIYLGSERALGVPDRFSGSGSGRDFTLKISRVEAQDVGTYYCLQTRQGAFTFGQGTKLEIKRTVAAPSVFIFPPSDSQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGECG |
Antigen
Chain: Y
Mutation: NULL
| >8GPG_Y|Chain G[auth X], H[auth Y], I[auth Z]|HIV-1 Env X18 UFO|Human immunodeficiency virus 1 (11676) NLWVTVYYGVPVWRDADTTLFCASDAKAHVPEAHNVWATHACVPTDPNPQEIPLENVTENFNMWKNNMVEQMQEDVISLWDQSLKPCVKLTPLCVTLNCTKANLTHNTTNDKNGTGNITDEVKIGNITDEVKNCTFNMTTEIRDKQQKVHALFYALDIVQMKENGSEYRLISCNTSVIKQACPKISFDPIPIHYCAPAGYAILKCNDKKFNGTGPCKNVSTVQCTHGIKPVVSTQLLLNGSLAEEEIIIRSENLTNNAKNIIVHLNKSVSISCTRPSNNTRTSIRIGPGQMFYRTGDIIGDIRKAYCELNGTEWNETLNKVTEKLKEHFNKTIVFQPPSGGDLETTMHHFNCRGEFFYCNTTKLFNTKNGTREEFNGTIILPCRIKQIVNMWQGVGQAMYAPPISGIINCTSNITGIILTRDGGNGNTTDETFRPGGGNIKDNWRSELYKYKVVQIEPLGIAPTRCKRRVVDGGGGSGGGGSAVGIGAMIFGFLGAAGSTMGAASITLTVQARQLLSGNPDWLPDMTVWGIKQLQARVLAVERYLKDQKFLGLWGCSGKIICCTNVPWNSTWSNKSYEEIWNNMTWIEWEKEISNYTNRIYDLLTESQNQQERNEKDLLELD |
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)
| Chain residues position delta_SASA
: residuesposition C: GLY26 VAL27 SER28 ARG30 GLY31 TYR32 ASP52 ARG99 LEU100 MET101 MET102 VAL103 ASP104 VAL106 HIS109 D: ARG32 ASN33 GLY34 ASP35 TYR54 LEU55 GLU58 ARG59 ALA60 LEU61 Y: THR37 TYR39 GLU87 ASN88 THR499 ARG500 CYS501 LYS502 ARG503 GLY521 GLY524 ALA525 SER528 THR529 GLY531 ALA532 SER534 ILE535 THR536 LEU537 LYS601 ILE603 CYS605 TYR619 GLU620 GLU621 TRP623 ASN624 ASN625 |
2、We defined interacting paratope-epitope residues by a distance cutoff of < 6 Å . Two amino acids are considered as interacting residues if they have at least one atom within a distance of 6 Å from any atom.
Interacting residues (Atom distance based)
