Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 6266 |
| PDBID: | 8GP5 |
| Chains: | EF_X |
| Organism: | Homo sapiens |
| Method: | EM |
| Resolution (Å): | 4.05 |
| 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: E
Mutation: NULL
| >8GP5_E|Chain A[auth E]|F6 Fab VH domain|Homo sapiens (9606) QVQLQQWGTGLLKPSETLSLTCAVYGVSLRGYYWTWIRQSPKKGLEWIGEIDEIGRTKYSQSLRSRATLSIDTSKKQFSLRLTSVTAADMATYYCARWRLMMVDEVTRHGMDVWSQGTMVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTHT |
Light Chain: F
Mutation: NULL
| >8GP5_F|Chain B[auth F]|F6 Fab VL domain|Homo sapiens (9606) DIVMTQSPLSLSVAPGEAASISCRSTQSLLNRNGDNYLEWYLRRPGRSPQLLIYLGSERALGVPDRFSGSGSGRDFTLKISRVEAQDVGTYYCLQTRQGAFTFGQGTKLEIKRTVAAPSVFIFPPSDSQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGECG |
Antigen
Chain: X
Mutation: NULL
| >8GP5_X|Chain C[auth X]|X18 UFO Env protomer|Homo sapiens (9606) 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 E: GLY26 VAL27 SER28 ARG30 GLY31 TYR32 TYR33 ARG96 LEU97 MET98 MET99 F: ASN28 GLY29 ASP30 TYR49 LEU50 GLU53 ARG54 ALA55 LEU56 X: ASN33 LEU34 THR37 TYR39 GLU87 ASN88 THR499 ARG500 CYS501 LYS502 GLY521 GLY524 ALA525 SER528 THR529 GLY531 ALA532 SER534 ILE535 THR536 LEU537 LYS601 ILE603 CYS604 CYS605 SER618 TYR619 GLU620 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)
