Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 6163 |
| PDBID: | 8EUW |
| Chains: | IJ_D |
| Organism: | Human immunodeficiency virus 1, Homo sapiens |
| Method: | EM |
| Resolution (Å): | 2.70 |
| Reference: | 10.1038/s41467-023-42098-5 |
| Antibody | |
| Antibody: | VRC34.01-MM28 Fab |
| Antibody mutation: | No |
| INN (Clinical Trial): | |
| Antigen | |
| Antigen: | HIV-1 BG505 DS-SOSIP spike glycoprotein - gp41 |
| Antigen mutation: | No |
| Durg Target: | |
Sequence information
Antibody
Heavy Chain: I
Mutation: NULL
| >8EUW_I|Chain G, I, K|VRC34.01-MM28 FAB variable heavy chain|Homo sapiens (9606) QKVLVQSGAEVKKPGASVKVSCRAFGYTFTGNPLHWVRQAPGQGLEWLGWINPHSGDTFTSQKFQGRVYMTRDKSINTAFLDVTRLTSDDTGIYYCARDKYYGNEAVGMDVWGQGTSVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPK |
Light Chain: J
Mutation: NULL
| >8EUW_J|Chain H, J, L|VRC34.01-MM28 FAB variable light chain|Homo sapiens (9606) DIQLTQSPSFLSASVGDKVTITCRASQGVRNELAWYQQKPGKAPNLLIYYASTLQSGVPSRFSATGSGTHFTLTVSSLQPEDFATYFCQHMSSYPLTFGGGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRG |
Antigen
Chain: D
Mutation: NULL
| >8EUW_D|Chain B, D, F|Envelope glycoprotein gp41|Human immunodeficiency virus 1 (11676) AVGIGAVFLGFLGAAGSTMGAASMTLTVQARNLLSGIVQQQSNLLRAPEAQQHLLKLTVWGIKQLQARVLAVERYLRDQQLLGIWGCSGKLICCTNVPWNSSWSNRNLSEIWDNMTWLQWDKEISNYTQIIYGLLEESQNQQEKNEQDLLALD |
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: THR28 THR30 GLY31 ASN32 PRO33 TRP50 ILE51 HIS53 SER54 ASP56 THR57 PHE58 TYR97 J: ARG30 GLU32 MET91 SER92 SER93 TYR94 LEU96 D: ALA512 VAL513 GLY514 ILE515 GLY516 ALA517 VAL518 PHE519 LEU520 GLY521 MET535 |
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)
