Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 1053 |
| PDBID: | 4XNZ |
| Chains: | HL_G |
| Organism: | Human immunodeficiency virus 1, Homo sapiens |
| Method: | XRD |
| Resolution (Å): | 3.39 |
| Reference: | 10.1016/j.cell.2015.03.004 |
| Antibody | |
| Antibody: | VRC06B Fab |
| Antibody mutation: | No |
| INN (Clinical Trial): | |
| Antigen | |
| Antigen: | HIV-1 clade A/E strain 93TH057 gp120 |
| Antigen mutation: | No |
| Durg Target: | |
Sequence information
Antibody
Heavy Chain: H
Mutation: NULL
| >4XNZ_H|Chain B, E, H|HEAVY CHAIN OF ANTIBODY VRC06B|Homo sapiens (9606) QVQLVESGSAMRKPGSSVKISCRASGFNFREYSIHWVRLIPGRGLEWMGWIKGMWGAVNYARQLQGRVSMTRQLSQDPDDPDWGVAYLDFSGLTSGDTGEYFCVRKGPSCPHCGDFHWQHWGQGTLVVVSTASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSC |
Light Chain: L
Mutation: NULL
| >4XNZ_L|Chain C, F, I[auth L]|LIGHT CHAIN OF ANTIBODY VRC06B|Homo sapiens (9606) EIVLTQSPGTLSVSPGERATLFCKASQGGNSLSWYQKRRGQPPRLLIYDTSRRASGIPDRFVGSGSGTDFSLTITKVDRDDFALYFCQQFEFFGLGTALEINRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC |
Antigen
Chain: G
Mutation: NULL
| >4XNZ_G|Chain A, D, G|Envelope glycoprotein gp160,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)
| Chain residues position delta_SASA
: residuesposition H: ARG30 SER33 TRP47 TRP50 MET53 TRP54 GLY55 ALA56 VAL57 ASN58 TYR59 ALA60 ARG61 GLN62 GLN64 ARG71 SER74 HIS101 GLY103 ASP104 PHE105 L: ILE2 GLN27 PHE90 GLU91 PHE92 G: LYS97 THR123 GLY124 ASN276 THR278 ASN279 ASN280 ALA281 LYS282 SER365 GLY366 GLY367 ASP368 GLU370 ILE371 ASN425 MET426 TRP427 GLY429 THR430 GLY431 THR455 ARG456 ASP457 GLY458 GLY459 ALA460 ASN461 ASN465 GLU466 THR467 ARG469 GLY471 GLY472 GLY473 ASN474 |
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)
