Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 1798 |
| PDBID: | 5V8M |
| Chains: | TR_F |
| Organism: | Human immunodeficiency virus 1, Homo sapiens |
| Method: | EM |
| Resolution (Å): | 4.40 |
| Reference: | 10.1016/j.immuni.2017.03.017 |
| Antibody | |
| Antibody: | 3BNC117 Fab |
| Antibody mutation: | No |
| INN (Clinical Trial): | |
| Antigen | |
| Antigen: | HIV-1 BG505 SOSIP.664 gp120 |
| Antigen mutation: | No |
| Durg Target: | |
Sequence information
Antibody
Heavy Chain: T
Mutation: NULL
| >5V8M_T|Chain D[auth L], H[auth T], L[auth U]|antibody 3BNC117, light chain|Homo sapiens (9606) DIQMTQSPSSLSASVGDTVTITCQANGYLNWYQQRRGKAPKLLIYDGSKLERGVPSRFSGRRWGQEYNLTINNLQPEDIATYFCQVYEFVVPGTRLDLKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC |
Light Chain: R
Mutation: NULL
| >5V8M_R|Chain C[auth H], G[auth R], K[auth S]|antibody 3BNC117, heavy chain|Homo sapiens (9606) QVQLLQSGAAVTKPGASVRVSCEASGYNIRDYFIHWWRQAPGQGLQWVGWINPKTGQPNNPRQFQGRVSLTRHASWDFDTYSFYMDLKALRSDDTAVYFCARQRSDYWDFDVWGSGTQVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSC |
Antigen
Chain: F
Mutation: NULL
| >5V8M_F|Chain A, E[auth F], I[auth G]|gp120|Human immunodeficiency virus 1 (11676) AENLWVTVYYGVPVWKDAETTLFCASDAKAYETEKHNVWATHACVPTDPNPQEIHLENVTEEFNMWKNNMVEQMHTDIISLWDQSLKPCVKLTPLCVTLQCTNVTNNITDDMRGELKNCSFNMTTELRDKKQKVYSLFYRLDVVQINENQGNRSNNSNKEYRLINCNTSAITQACPKVSFEPIPIHYCAPAGFAILKCKDKKFNGTGPCPSVSTVQCTHGIKPVVSTQLLLNGSLAEEEVMIRSENITNNAKNILVQFNTPVQINCTRPNNNTRKSIRIGPGQAFYATGDIIGDIRQAHCNVSKATWNETLGKVVKQLRKHFGNNTIIRFANSSGGDLEVTTHSFNCGGEFFYCNTSGLFNSTWISNTSVQGSNSTGSNDSITLPCRIKQIINMWQRIGQAMYAPPIQGVIRCVSNITGLILTRDGGSTNSTTETFRPGGGDMRDNWRSELYKYKVVKIEPLGVAPTRCKRRVVGRRRRRR |
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)
| R: ARG30 PHE33 TRP47 TRP50 LYS53 THR54 GLY55 GLN56 PRO57 ASN58 ASN59 PRO60 ARG61 GLN64 TRP71 PHE73 GLN95 ASP98 T: ASP1 ILE2 GLN3 TYR32 TYR91 GLU96 PHE97 F: ASN197 THR198 ASN276 THR278 ASN279 ASN280 ALA281 LYS282 ARG360 SER364 SER365 GLY366 GLY367 ASP368 VAL371 GLN428 ILE430 THR455 ARG456 ASP457 GLY458 GLY459 SER460 THR461 ASN462 SER463 THR464 THR465 THR467 ARG469 PRO470 GLY471 GLY472 ASP474 ARG476 |
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)
