Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 3093 |
| PDBID: | 6W4M |
| Chains: | HL_G |
| Organism: | Human immunodeficiency virus 1, Homo sapiens, synthetic construct |
| Method: | XRD |
| Resolution (Å): | 3.20 |
| Reference: | 10.1186/s12915-020-00819-y |
| Antibody | |
| Antibody: | N12-I2 Fab |
| Antibody mutation: | No |
| INN (Clinical Trial): | |
| Antigen | |
| Antigen: | HIV-1 clade A/E 93TH057 gp120 |
| Antigen mutation: | Yes |
| Durg Target: | |
Sequence information
Antibody
Heavy Chain: H
Mutation: NULL
| >6W4M_H|Chain C[auth H]|ANTI-HIV ANTIBODY N12-I2 FAB HEAVY CHAIN|Homo sapiens (9606) QVQLVQSGAEVKKPGSSVKVSCRASRGTFSSYGITWVRQAPGQGLEWMGGIIPIFDVTNYAQNFQGRVAITTDAEMSTAYMELRSLKSEDSAVYYCASDSRDFSYYEPGTSYSHYYNIMDVWGQGTTVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSCDKTH |
Light Chain: L
Mutation: NULL
| >6W4M_L|Chain B[auth L]|ANTI-HIV ANTIBODY N12-I2 FAB LIGHT CHAIN|Homo sapiens (9606) EIVMMQSPGTLSLSPGERATLSCRASQSVSSSYLAWYQQKPGQAPRLLIYGASSRATGIPDRFSGSGSGTDFTLTISRLEPEDFAVYYCQQYGSSPETFGQGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC |
Antigen
Chain: G
Mutation: H242S
| >6W4M_G|Chain A[auth G]|clade A/E 93TH057 HIV-1 gp120 core|Human immunodeficiency virus 1 (11676) VWKDADTTLFCASDAKAHETEVHNVWATHACVPTDPNPQEIHLENVTENFNMWKNNMVEQMQEDVISLWDQSLQPCVKLTGGSVIKQACPKISFDPIPIHYCTPAGYVILKCNDKNFNGTGPCKNVSSVQCTHGIKPVVSTQLLLNGSLAEEEIIIRSENLTNNAKTIIVHLNKSVEINCTRPSNGGSGSGGDIRKAYCEINGTKWNKVLKQVTEKLKEHFNNKTIIFQPPSGGDLEITMHSFNCRGEFFYCNTTQLFNNTCIGNETMKGCNGTITLPCKIKQIINMWQGTGQAMYAPPIDGKINCVSNITGILLTRDGGANNTSNETFRPGGGNIKDNWRSELYKYKVVQIE |
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)
| L: SER31 TYR32 H: ARG26 GLY27 THR28 SER30 SER31 TYR32 PRO52 ILE53 PHE54 GLU74 ARG97 ASP98 PHE99 G: CYS119 VAL120 LEU122 VAL200 LYS202 GLN203 CYS205 ASN301 GLY324 ASP325 ILE326 ARG327 LYS419 LYS421 GLN422 ILE423 GLN432 MET434 TYR435 ALA436 PRO437 |
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)
