Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 6236 |
| PDBID: | 8G4T |
| Chains: | JK_B |
| Organism: | Human immunodeficiency virus 1, Homo sapiens |
| Method: | EM |
| Resolution (Å): | 2.81 |
| Reference: | 10.1016/j.celrep.2023.112755 |
| Antibody | |
| Antibody: | 2C09 Fab |
| Antibody mutation: | No |
| INN (Clinical Trial): | |
| Antigen | |
| Antigen: | HIV-1 BG505 DS-SOSIP envelope glycoprotein - gp41 |
| Antigen mutation: | Yes |
| Durg Target: | |
Sequence information
Antibody
Heavy Chain: J
Mutation: NULL
| >8G4T_J|Chain G[auth D], I[auth H], K[auth J]|Fab 2C09 heavy chain|Homo sapiens (9606) EVQLVESGEGLVQPGGSLRLSCAASGFTFSSHAMHWVRQAPGKGLEYVSAISSEGGSTYYADSVRGRFIISRDNSKNTLYLQMGSLRAEDMAVYYCARVTGDYNWYFDLWGRGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKGLEVLFQ |
Light Chain: K
Mutation: NULL
| >8G4T_K|Chain H[auth E], J[auth K], L|Fab 2C09 light chain|Homo sapiens (9606) EIVMTQSPATLSVSPGERATLSCRASQGVSSNLAWYQQKPGQAPRLLIHGASTRATGSPARFSGSGSGTEFTLTISSLQSEDFAVYSCQQYHNWPWTFGQGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC |
Antigen
Chain: B
Mutation: T94C
| >8G4T_B|Chain A, B, D[auth F]|Envelope glycoprotein BG505 DS-SOSIP gp41|Human immunodeficiency virus 1 (11676) AVGIGAVFLGFLGAAGSTMGAASMTLTVQARNLLSGIVQQQSNLLRAIEAQQHLLKLTVWGIKQLQARVLAVERYLRDQQLLGIWGCSGKLICCTNVPWNSSWSNRNLSEIWDNMTWLQWDKEISNYTQIIYGLLEESQNQQEKNEQDLLALD |
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)
| J: SER31 HIS32 ALA33 HIS35 ALA50 ILE51 SER52 GLU53 GLY55 SER56 TYR58 VAL95 GLY97 ASP98 TYR99 K: TRP94 TRP96 B: ALA512 VAL513 GLY514 ILE515 GLY516 ALA517 VAL518 PHE519 LEU520 SER528 ALA532 MET535 VAL539 ARG542 |
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)
