Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 1835 |
| PDBID: | 5VN3 |
| Chains: | MO_J |
| Organism: | Homo sapiens, Human immunodeficiency virus 1 |
| Method: | EM |
| Resolution (Å): | 3.70 |
| Reference: | 10.1038/nature23010 |
| Antibody | |
| Antibody: | 17b Fab |
| Antibody mutation: | No |
| INN (Clinical Trial): | |
| Antigen | |
| Antigen: | HIV-1 B41 SOSIP.664 gp160 |
| Antigen mutation: | Yes |
| Durg Target: | P00750 |
Sequence information
Antibody
Heavy Chain: M
Mutation: NULL
| >5VN3_M|Chain E[auth H], J[auth K], O[auth M]|17b Fab heavy chain|Homo sapiens (9606) QVQLLESGAEVKKPGSSVKVSCKASGDTFIRYSFTWVRQAPGQGLEWMGRIITILDVAHYAPHLQGRVTITADKSTSTVYLELRNLRSDDTAVYFCAGVYEGEADEGEYDNNGFLKHWGQGTLVTVTSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPK |
Light Chain: O
Mutation: NULL
| >5VN3_O|Chain A[auth L], F[auth N], K[auth O]|17b Fab light chain|Homo sapiens (9606) ELELTQSPATLSVSPGERATLSCRASESVSSDLAWYQQKPGQAPRLLIYGASTRATGVPARFSGSGSGAEFTLTISSLQSEDFAVYYCQQYNNWPPRYTFGQGTRLEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRG |
Antigen
Chain: J
Mutation: A512C
| >5VN3_J|Chain C[auth G], H[auth I], M[auth J]|Envelope glycoprotein gp160|Human immunodeficiency virus 1 (11676) MDAMKRGLCCVLLLCGAVFVSPSQEIHARFRRGARAAKKWVTVYYGVPVWKEATTTLFCASDAKAYDTEVHNVWATHACVPTDPNPQEIVLGNVTENFNMWKNNMVEQMHEDIISLWDQSLKPCVKLTPLCVTLNCNNVNTNNTNNSTNATISDWEKMETGEMKNCSFNVTTSIRDKIKKEYALFYKLDVVPLENKNNINNTNITNYRLINCNTSVITQACPKVSFEPIPIHYCAPAGFAILKCNSKTFNGSGPCTNVSTVQCTHGIRPVVSTQLLLNGSLAEEEIVIRSENITDNAKTIIVQLNEAVEINCTRPNNNTRKSIHIGPGRAFYATGDIIGNIRQAHCNISKARWNETLGQIVAKLEEQFPNKTIIFNHSSGGDPEIVTHSFNCGGEFFYCNTTPLFNSTWNNTRTDDYPTGGEQNITLQCRIKQIINMWQGVGKAMYAPPIRGQIRCSSNITGLLLTRDGGRDQNGTETFRPGGGNMRDNWRSELYKYKVVKIEPLGIAPTACKRRV |
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)
| O: SER30 SER31 TYR49 THR53 THR56 TRP94 M: GLN1 VAL2 ILE53 LEU54 ASP55 VAL56 HIS58 TYR96 GLY98 LYS101 HIS102 J: CYS119 VAL120 LEU122 VAL200 THR202 GLN203 ALA204 CYS205 LYS305 SER306 HIS308 ILE309 ASN325 ARG327 PRO369 ARG419 ILE420 LYS421 GLN422 ILE423 LYS432 ALA433 MET434 TYR435 PRO437 ARG440 |
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)
