Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 594 |
| PDBID: | 3NGB |
| Chains: | JK_I |
| Organism: | Human immunodeficiency virus 1, Homo sapiens |
| Method: | XRD |
| Resolution (Å): | 2.68 |
| Reference: | 10.1126/science.1192819 |
| Antibody | |
| Antibody: | VRC01 Fab |
| Antibody mutation: | No |
| INN (Clinical Trial): | |
| Antigen | |
| Antigen: | HIV-1 gp120 |
| Antigen mutation: | No |
| Durg Target: | |
Sequence information
Antibody
Heavy Chain: J
Mutation: NULL
| >3NGB_J|Chain B, E, H, K[auth J]|Antigen binding fragment of heavy chain: Antibody VRC01|Homo sapiens (9606) QVQLVQSGGQMKKPGESMRISCRASGYEFIDCTLNWIRLAPGKRPEWMGWLKPRGGAVNYARPLQGRVTMTRDVYSDTAFLELRSLTVDDTAVYFCTRGKNCDYNWDFEHWGRGTPVIVSSPSTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKAEPKSC |
Light Chain: K
Mutation: NULL
| >3NGB_K|Chain C, F, I[auth K], L|Antigen binding fragment of light chain: Antibody VRC01|Homo sapiens (9606) EIVLTQSPGTLSLSPGETAIISCRTSQYGSLAWYQQRPGQAPRLVIYSGSTRAAGIPDRFSGSRWGPDYNLTISNLESGDFGVYYCQQYEFFGQGTKVQVDIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLRSPVTKSFNRGEC |
Antigen
Chain: I
Mutation: NULL
| >3NGB_I|Chain A, D, G, J[auth I]|Envelope glycoprotein gp160|Human immunodeficiency virus 1 (11676) VWKDADTTLFCASDAKAHETEVHNVWATHACVPTDPNPQEIHLENVTENFNMWKNNMVEQMQEDVISLWDQSLQPCVKLTGGSVIKQACPKISFDPIPIHYCTPAGYVILKCNDKNFNGTGPCKNVSSVQCTHGIKPVVSTQLLLNGSLAEEEIIIRSENLTNNAKTIIVHLNKSVEINCTRPSNGGSGSGGDIRKAYCEINGTKWNKVLKQVTEKLKEHFNNKTIIFQPPSGGDLEITMHHFNCRGEFFYCNTTQLFNNTCIGNETMKGCNGTITLPCKIKQIINMWQGTGQAMYAPPIDGKINCVSNITGILLTRDGGANNTSNETFRPGGGNIKDNWRSELYKYKVVQIE |
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)
| J: ILE30 THR33 TRP47 TRP50 ARG53 GLY54 GLY55 ALA56 VAL57 ASN58 TYR59 ALA60 ARG61 PRO62 GLN64 ARG71 VAL73 TYR74 ASP99 K: ILE2 VAL3 GLN27 TYR91 GLU96 PHE97 I: LYS97 GLY124 GLY198 ASN276 THR278 ASN279 ASN280 ALA281 LYS282 THR283 SER365 GLY366 GLY367 ASP368 ILE371 TRP427 GLN428 GLY429 THR430 THR455 ARG456 ASP457 GLY458 GLY459 ALA460 ASN461 ASN462 ASN465 GLU466 THR467 ARG469 GLY472 GLY473 ASN474 |
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)
