Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 1517 |
| PDBID: | 5KJR |
| Chains: | HL_G |
| Organism: | Human immunodeficiency virus 1, synthetic construct, Homo sapiens |
| Method: | XRD |
| Resolution (Å): | 2.98 |
| Reference: | 10.1128/JVI.01068-16 |
| Antibody | |
| Antibody: | N60-I3 Fab |
| Antibody mutation: | No |
| INN (Clinical Trial): | |
| Antigen | |
| Antigen: | HIV-1 clade A/E 93TH057 gp120 |
| Antigen mutation: | No |
| Durg Target: | |
Sequence information
Antibody
Heavy Chain: H
Mutation: NULL
| >5KJR_H|Chain C[auth H]|N60-I3 FAB HEAVY CHAIN|Homo sapiens (9606) EVQLVESGPGLVKPSQTLSLTCTVSGASISSGGYFWSWIRQHPGKGLEWIGNIYYIGNTYYNPSLKSRLTISVDTTQNQFSLKLTSVTAADTAVYYCARVPRLRGGNYFDSWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSCDKTH |
Light Chain: L
Mutation: NULL
| >5KJR_L|Chain D[auth L]|N60-I3 FAB LIGHT CHAIN|Homo sapiens (9606) TGVLSQSVLTQPASVSGSPGQSITISCTGTSSDVGGYKYVSWYQQHPDKAPKLMIYEVSNRPSGVSNRFSGSKSGNTASLTISGLQAEDEADYYCSSYTSSSTWVFGGGTKLTVLGQPKAAPSVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSYLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPTECS |
Antigen
Chain: G
Mutation: NULL
| >5KJR_G|Chain A[auth G]|clade A/E 93TH057 HIV-1 gp120 core|Human immunodeficiency virus 1 (11676) VWKDADTTLFCASDAKAHETEVHNVAATHACVPTDPNPQEIHLENVTENFNMWKNNMVEQMQEDVISLWDQWLQPCVKLTGGSVIKQACPKISFDPIPIHYCTPAGYVILKCNDKNFNGTGPCKNVSSVQCTHGIKPVVSTQLLLNGSLAEEEIIIRSENLTNNAKTIIVHLNKSVEINCTRPSNGGSGSGGDIRKAYCEINGTKWNKVLKQVTEKLKEHFNNKTIIFQPPSGGDLEITMHSFNCRGEFFYCNTTQLFNNTCIGNETMKGCNGTITLPCKIKQIINMWQGTGQAMYAPPIDGKINCVSNITGILLTRDGGANNTSNETFRPGGGNIKDNWRSELYKYKVVQIE |
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)
| H: ALA27 SER28 SER31 GLY32 GLY33 TYR34 TYR52 TYR53 ILE54 ASN56 TYR58 ARG97 LEU98 ARG99 L: GLY29 TYR30 TYR32 TYR91 G: THR51 LEU52 PHE53 CYS54 ALA60 VAL68 THR71 HIS72 ALA73 CYS74 VAL75 PRO76 THR77 ASP78 PRO79 GLN103 GLU106 ASP107 GLN114 TRP115 TYR217 THR219 PRO220 ALA221 |
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)
