Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 1360 |
| PDBID: | 5FYJ |
| 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 clade G X1193.c1 SOSIP.664 gp120 |
| Antigen mutation: | No |
| Durg Target: | |
Sequence information
Antibody
Chain: U
Mutation: NULL
| >5FYJ_U|Chain G[auth U], H[auth V]|VRC01|HOMO SAPIENS (9606) EIVLTQSPGTLSLSPGETAIISCRTSQYGSLAWYQQRPGQAPRLVIYSGSTRAAGIPDRFSGSRWGPDYNLTISNLESGDFGVYYCQQYEFFGQGTKVQVGGGGSGGGGSGGGGSQVQLVQSGGQMKKPGESMRISCRASGYEFIDCTLNWIRLAPGKRPEWMGWLKPRGGAVNYCRPLQGRVTMTRDVYSDTAFLELRSLTVDDTAVYFCTRGKNCDYNWDFEHWGRGTPVIVGGLVPR |
Antigen
Chain: G
Mutation: NULL
| >5FYJ_G|Chain D[auth G]|GP120 ENV ECTODOMAIN|HUMAN IMMUNODEFICIENCY VIRUS 1 (11676) ALAGDLWVTVYYGVPVWEDADTTLFCASDAKAYSTESHNVWATHACVPTDPNPQEIPLKNVTENFNMWKNNMVEQMHEDIISLWDESLKPCVKLTPLCVTLICTNVTSNSTNSTNGVTNNSTVDYREQLKNCSFNITTEIRDKQRKEYALFYRLDIVPINDNEKNDTYRLINCNVSTIKQACPKVTFDPIPIHYCAPAGFAILKCRDKKFNGTGPCKNVSTVQCTHGIKPVISTQLLLNGSLAEGDIMIRSENITDNAKTIIVQLKTAVNITCTRPSNNTRKSIRFGPGQAFYATDEIIGDIRQAHCNISKTEWEDMKRNVSDKLKALFNNKTIIFKSSSGGDLEITTHSFNCRGEFFYCNTSGLFNTSGLFNNNSNDSSGNITLPCKIKQIVRMWQRVGQAMYAPPIAGNITCRSRITGLLLVRDGCKSNETNGTETFRPAGGDMRDNWRSELYKYKVVKIKPLGVAPTRCRRRVVGRRRRRR |
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 U: GLU28 ILE30 THR33 TRP47 TRP50 ARG53 GLY54 GLY55 ALA56 VAL57 ASN58 TYR59 CYS60 ARG61 PRO62 GLN64 ARG71 VAL73 TYR74 ASP76 CYS98 ASP99 G: TRP96 LYS97 VAL198 GLU275 ASP279 ASN280 ALA281 LYS282 THR283 ILE360 SER365 GLY366 GLY367 ASP368 ILE371 ARG425 GLN428 ARG429 VAL455 ARG456 ASP457 GLY458 CYS459 LYS460 SER461 THR465 GLU466 THR467 ARG469 ALA471 GLY473 ASP474 ARG476 |
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)
