Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 1885 |
| PDBID: | 5W4L |
| Chains: | DE_G |
| Organism: | Human immunodeficiency virus 1, synthetic construct, Homo sapiens |
| Method: | XRD |
| Resolution (Å): | 2.92 |
| Reference: | 10.1016/j.str.2017.09.009 |
| Antibody | |
| Antibody: | N12-i3 Fab |
| Antibody mutation: | No |
| INN (Clinical Trial): | |
| Antigen | |
| Antigen: | HIV-1 clade A/E 93TH05 gp120 |
| Antigen mutation: | Yes |
| Durg Target: | |
Sequence information
Antibody
Heavy Chain: D
Mutation: NULL
| >5W4L_D|Chain E[auth B], K[auth D]|Antibody N12-i3 Fab heavy chain|Homo sapiens (9606) QVQLVQSGAEVKKPGSSVRVSCKASGGSFSRYTVNWVRQAPGQGLEWMARFIPIFNMPDYAPKFQGRITITADESTSTAYLELSSLTSDDTAVYYCASRQHHEYFQEWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSCDKTH |
Light Chain: E
Mutation: NULL
| >5W4L_E|Chain F[auth C], L[auth E]|Antibody N12-i3 light chain|Homo sapiens (9606) EIVLTQSPGTLSMSPGERATLSCRASRTVSSSNLAWYQQKPGQAPRLLIYDVSSRATGIPDRFSGRGSGTDFTLTISRLEPEDFAVYYCQQYGTSPLTFGGGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC |
Antigen
Chain: G
Mutation: H255S
| >5W4L_G|Chain A, G|clade A/E 93TH057 HIV-1 gp120 core|Human immunodeficiency virus 1 (11676) SDNLWVTVYYGVPVWKDADTTLFCASDAKAHETEVHNVWATHACVPTDPNPQEIHLENVTENFNMWKNNMVEQMQEDVISLWDQSLQPCVKLTGGSVIKQACPKISFDPIPIHYCTPAGYVILKCNDKNFNGTGPCKNVSSVQCTHGIKPVVSTQLLLNGSLAEEEIIIRSENLTNNAKTIIVHLNKSVEINCTRPSNGGSGSGGDIRKAYCEINGTKWNKVLKQVTEKLKEHFNNKTIIFQPPSGGDLEITMHSFNCRGEFFYCNTTQLFNNTCIGNETMKGCNGTITLPCKIKQIINMWQGTGQAMYAPPIDGKINCVSNITGILLTRDGGANNTSNETFRPGGGNIKDNWRSELYKYKVVQIEPLGIAPTKAKRRVVQREKR |
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 D: SER28 SER30 TYR32 THR33 ARG50 PRO52 ILE53 PHE54 MET56 PRO57 ASP58 ARG95 GLN96 HIS97 HIS98 GLU99 E: ASN32 TYR91 GLY92 THR93 SER94 LEU96 G: SER31 ASP32 LEU34 TRP35 VAL36 THR37 VAL38 TYR39 TYR40 VAL42 PRO43 TRP45 GLN82 ILE84 HIS85 LEU86 GLU87 VAL224 SER244 VAL245 GLN246 ILE491 |
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)
