Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 6508 |
| PDBID: | 7RAI |
| Chains: | IM_C |
| Organism: | Human immunodeficiency virus 1, Homo sapiens |
| Method: | EM |
| Resolution (Å): | 3.24 |
| Reference: | 10.1038/s41467-021-26846-z |
| Antibody | |
| Antibody: | M4008_N1 Fab |
| Antibody mutation: | No |
| INN (Clinical Trial): | |
| Antigen | |
| Antigen: | HIV BG505 DS-SOSIP.664 Envelope glycoprotein gp160 |
| Antigen mutation: | Yes |
| Durg Target: | |
Sequence information
Antibody
Heavy Chain: I
Mutation: NULL
| >7RAI_I|Chain C[auth H], G[auth I], K[auth J]|M4008_N1 Fab heavy chain|Homo sapiens (9606) QSQLVQSGAEMKTSGSSVRVSCKDSGGFFPYAGFRWVRQAPGQGFEWMGGVIPADGTKHYAPKFQARMKMTVVESSRTLYMELRSLTSTDTATYFCARLQCAGFSCEMDSGPFDLWGQGTQVTVPSSGASASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSCDKTHTCPPCPAPELLGGPSVFLFPQNPRKPS |
Light Chain: M
Mutation: NULL
| >7RAI_M|Chain D[auth L], H[auth M], L[auth N]|M4008_N1 Fab light chain|Homo sapiens (9606) DIQMTQSPSTVAAFVGGNVTLSCRTSQGVGNRLAWYQQKPGKPPRLLISRASNRHGGVPARFSGGGSGTIFTLTIKGLQSDDFATFFCQQYYDSRETFGQGSRVMMEKIRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC |
Antigen
Chain: C
Mutation: I171C/T301N/A401C/A469C
| >7RAI_C|Chain A, E[auth C], I[auth E]|Envelope glycoprotein gp160|Human immunodeficiency virus 1 (11676) AENLWVTVYYGVPVWKDAETTLFCASDAKAYETEKHNVWATHACVPTDPNPQEIHLENVTEEFNMWKNNMVEQMHTDIISLWDQSLKPCVKLTPLCVTLQCTNVTNNITDDMRGELKNCSFNMTTELRDKKQKVYSLFYRLDVVQINENQGNRSNNSNKEYRLINCNTSACTQACPKVSFEPIPIHYCAPAGFAILKCKDKKFNGTGPCPSVSTVQCTHGIKPVVSTQLLLNGSLAEEEVMIRSENITNNAKNILVQFNTPVQINCTRPNNNTRKSIRIGPGQAFYATGDIIGDIRQAHCNVSKATWNETLGKVVKQLRKHFGNNTIIRFANSSGGDLEVTTHSFNCGGEFFYCNTSGLFNSTWISNTSVQGSNSTGSNDSITLPCRIKQIINMWQRIGQCMYAPPIQGVIRCVSNITGLILTRDGGSTNSTTETFRPGGGDMRDNWRSELYKYKVVKIEPLGVAPTRCKRRVVGR |
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)
| I: PHE28 PRO30 TYR31 PRO52 ALA53 ASP54 GLY55 THR56 GLU73 GLY99 M: ARG32 ARG50 TYR92 SER94 C: LYS65 THR163 GLU164 GLN170 VAL172 PRO206 LYS207 ASN301 THR303 ARG304 LYS305 SER306 ILE307 ARG308 GLY314 GLN315 ALA316 TYR318 ASP321 ILE323 GLY324 GLN440 |
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)
