Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 4359 |
| PDBID: | 7MXD |
| Chains: | XY_F |
| Organism: | Human immunodeficiency virus 1, Homo sapiens, Macaca mulatta |
| Method: | EM |
| Resolution (Å): | 3.40 |
| Reference: | 10.1002/advs.202200063 |
| Antibody | |
| Antibody: | J038 Fab |
| Antibody mutation: | No |
| INN (Clinical Trial): | |
| Antigen | |
| Antigen: | HIV-1 envelope glycoprotein -gp120 |
| Antigen mutation: | No |
| Durg Target: | |
Sequence information
Antibody
Heavy Chain: X
Mutation: NULL
| >7MXD_X|Chain J[auth X]|J038 antibody heavy chain|Macaca mulatta (9544) QLHLQESGPGLVRPSETLSLTCDVSGGAFNDAYCSWIRRFPGGGLEWIGRISGRDGYVESNPALTGRVTMSIDATWKKIVLRLTSMTASDTATYFCAGETPEDDFGYYQPYFKTWGQGLGVTVSSASTKGPSVFPLAPCSRSTSESTAALGCLVKDYFPEPVTVSWNSGSLTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYVCNVNHKPSNTKVDKRVEIKTC |
Light Chain: Y
Mutation: NULL
| >7MXD_Y|Chain K[auth Y]|J038 antibody light chain|Macaca mulatta (9544) DIQLIQSPSSVSASLGDRVTITCRSTQGIGSDLAWYQATPGTAPKLLIYNSFALHKGVPSRFSGSGSGTEFSLTITGLQPEDFATYYCQHYRRLPLTFGGGTNIEVKRAVAAPSVFIFPPSEDQVKSGTVSVVCLLNNFYPREASVKWKVDGVLKTGNSQESVTEQDSKDNTYSLSSTLTLSNTDYQSHNVYACEVTHQGLSSPVTKSFNRGEC |
Antigen
Chain: F
Mutation: NULL
| >7MXD_F|Chain A, D[auth F], E[auth G]|Envelope glycoprotein gp120|Human immunodeficiency virus 1 (11676) AENLWVTVYYGVPVWKDADTTLFCASDAKAHETEAHNIWATHACVPTDPNPQEIYMENVTENFNMWKNNMVEQMQEDIISLWDQSLKPCVKLTPLCVTLSCTNVTLTNVNYTNNFPNIGNITDEVRNCSFNVTTEIRDKKQKVYALFYKLDIVQMENKNSYRLINCNTSVCKQACPKISFDPIPIHYCTPAGYAILKCNEKNFNGTGPCKNVSSVQCTHGIKPVVSTQLLLNGSLAEGEIIIRSENLTNNAKTIIVHLNKSVEINCTRPSNNTRTSVTIGPGQVFYRTGDIIGDIRKAYCEINGTKWNETLKQVVGKLKEHFPNKTISFQPPSGGDLEITMHHFNCRGEFFYCNTTQLFNSTWINSTTIKEYNDTIIYLPCKIKQIINMWQGVGQCMYAPPIRGKINCVSNITGILLTRDGGDANATNDTETFRPGGGNIKDNWRSELYKYKVVQIEPLGIAPTKCKRRVVERRRRRR |
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 X: TYR33 ARG50 SER52 ARG54 ASP55 TYR57 GLU59 ASP103 ASP104 PHE105 GLY106 TYR107 TYR108 GLN109 PRO110 Y: ASP32 TYR91 ARG92 ARG93 LEU94 LEU96 F: SER130 ASN160 THR163 GLU164 ILE165 ARG166 ASP167 LYS168 LYS169 GLN170 LYS171 TYR173 |
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)
