Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 3005 |
| PDBID: | 6VI0 |
| Chains: | ED_C |
| Organism: | Human immunodeficiency virus 1, Homo sapiens |
| Method: | EM |
| Resolution (Å): | 3.43 |
| Reference: | 10.1080/19420862.2021.1946918 |
| Antibody | |
| Antibody: | VRC01.23 Fab |
| Antibody mutation: | No |
| INN (Clinical Trial): | |
| Antigen | |
| Antigen: | HIV-1 BG505 DS.SOSIP gp120 |
| Antigen mutation: | No |
| Durg Target: | |
Sequence information
Antibody
Heavy Chain: E
Mutation: NULL
| >6VI0_E|Chain D[auth E], H, L[auth K]|VRC01.23 Heavy chain|Homo sapiens (9606) QVQLVQSGGQMKKPGESMRISCRASGYEFIDCTLNWIRLAPGKRPEWMGWLKPRWGAVNYARPLQGRVTMTRQLSQDPDDPDWGTAFLELRSLTVDDTAVYFCTRGKNCDYNWDFEHWGRGTPVIVSSPSTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPK |
Light Chain: D
Mutation: NULL
| >6VI0_D|Chain C[auth D], G[auth J], K[auth L]|VRC01.23 Light chain|Homo sapiens (9606) LTQSPGTLSLSPGETAIISCRTSQYGSLAWYQQRPGQAPRLVIYSGSTRAAGIPDRFSGSRWGPDYNLTISNLESGDFGVYYCQQYEFFGQGTKVQVDIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC |
Antigen
Chain: C
Mutation: NULL
| >6VI0_C|Chain B[auth C], F[auth G], J[auth I]|BG505 gp120|Human immunodeficiency virus 1 (11676) AENLWVTVYYGVPVWKDAETTLFCASDAKAYETEKHNVWATHACVPTDPNPQEIHLENVTEEFNMWKNNMVEQMHTDIISLWDQSLKPCVKLTPLCVTLQCTNVTNNITDDMRGELKNCSFNMTTELRDKKQKVYSLFYRLDVVQINENQGNRSNNSNKEYRLINCNTSACTQACPKVSFEPIPIHYCAPAGFAILKCKDKKFNGTGPCPSVSTVQCTHGIKPVVSTQLLLNGSLAEEEVMIRSENITNNAKNILVQFNTPVQINCTRPNNNTRKSIRIGPGQAFYATGDIIGDIRQAHCNVSKATWNETLGKVVKQLRKHFGNNTIIRFANSSGGDLEVTTHSFNCGGEFFYCNTSGLFNSTWISNTSVQGSNSTGSNDSITLPCRIKQIINMWQRIGQCMYAPPIQGVIRCVSNITGLILTRDGGSTNSTTETFRPGGGDMRDNWRSELYKYKVVKIEPLGVAPTRCKRRVVGRRRRRR |
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)
| D: GLN27 TYR28 TYR91 GLU97 PHE98 E: ILE30 THR33 ARG44 TRP47 TRP50 ARG53 TRP54 GLY55 ALA56 VAL57 ASN58 TYR59 ALA60 ARG61 PRO62 GLN64 ARG71 LEU73 SER74 GLN75 ASP99 C: LYS97 HIS105 ASN197 THR198 ASN276 THR278 ASN279 ASN280 ALA281 LYS282 ASN283 SER365 GLY366 GLY367 ASP368 GLU370 VAL371 ASN425 MET426 TRP427 GLN428 ARG429 ILE430 GLY431 THR455 ARG456 ASP457 GLY458 GLY459 SER460 THR461 ASN462 THR465 GLU466 THR467 ARG469 GLY471 GLY472 GLY473 ASP474 MET475 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)
