Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 1363 |
| PDBID: | 5FYK |
| Chains: | U_G |
| Organism: | Human immunodeficiency virus 1, Homo sapiens |
| Method: | XRD |
| Resolution (Å): | 3.11 |
| Reference: | 10.1016/j.cell.2016.04.010 |
| Antibody | |
| Antibody: | VRC01 scFv |
| Antibody mutation: | No |
| INN (Clinical Trial): | |
| Antigen | |
| Antigen: | HIV-1 JR-FL gp120 |
| Antigen mutation: | No |
| Durg Target: | |
Sequence information
Antibody
Chain: U
Mutation: NULL
| >5FYK_U|Chain G[auth U], H[auth V]|VRC01|HOMO SAPIENS (9606) EIVLTQSPGTLSLSPGETAIISCRTSQYGSLAWYQQRPGQAPRLVIYSGSTRAAGIPDRFSGSRWGPDYNLTISNLESGDFGVYYCQQYEFFGQGTKVQVGGGGSGGGGSGGGGSQVQLVQSGGQMKKPGESMRISCRASGYEFIDCTLNWIRLAPGKRPEWMGWLKPRGGAVNYCRPLQGRVTMTRDVYSDTAFLELRSLTVDDTAVYFCTRGKNCDYNWDFEHWGRGTPVIVGGLVPR |
Antigen
Chain: G
Mutation: NULL
| >5FYK_G|Chain D[auth G]|JR-FL, GP120 ENV ECTODOMAIN|HUMAN IMMUNODEFICIENCY VIRUS 1 (11676) VEKLWVTVYYGVPVWKEATTTLFCASDAKAYDTEVHNVWATHACVPTDPNPQEVVLENVTEHFNMWKNNMVEQMQEDIISLWDQSLKPCVKLTPLCVTLNCKDVNATNTTNDSEGTMERGEIKNCSFNITTSIRDKVQKEYALFYKLDVVPIDNNNTSYRLISCDTSVITQACPKISFEPIPIHYCAPAGFAILKCNDKTFNGKGPCKNVSTVQCTHGIRPVVSTQLLLNGSLAEEEVVIRSDNFTNNAKTIIVQLKESVEINCTRPNNNTRKSIHIGPGRAFYTTGEIIGDIRQAHCNISRAKWNDTLKQIVIKLREQFENKTIVFNHSSGGDPEIVMHSFNCGGEFFYCNSTQLFNSTWNNNTEGSNNTEGNTITLPCRIKQIINMWQEIGKAMYAPPIRGQIRCSSNITGLLLTRDGCINENGTEIFRPGGGDMRDNWRSELYKYKVVKIEPLGVAPTKCKRRVVGRRRRRR |
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)
| U: ILE30 ASP31 THR33 TRP47 TRP50 ARG53 GLY54 GLY55 ALA56 VAL57 ASN58 TYR59 CYS60 ARG61 PRO62 GLN64 ARG71 TYR74 ASP99 G: LYS97 GLN105 ILE109 THR198 SER199 ASP275 ASN279 ASN280 ALA281 THR283 SER365 GLY366 GLY367 ASP368 GLU370 ILE371 TRP427 GLN428 GLY431 THR455 ARG456 ASP457 GLY458 CYS459 ILE460 ASN461 GLY464 THR465 GLU466 ILE467 ARG469 GLY471 GLY472 GLY473 ASP474 MET475 ARG476 |
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)
