Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 2979 |
| PDBID: | 6V8X |
| Chains: | CD_A |
| Organism: | Human immunodeficiency virus 1, Homo sapiens |
| Method: | EM |
| Resolution (Å): | 3.00 |
| Reference: | 10.1038/s41467-019-14196-w |
| Antibody | |
| Antibody: | VRC01 Fab |
| Antibody mutation: | No |
| INN (Clinical Trial): | |
| Antigen | |
| Antigen: | HIV-1 BG505 gp120 |
| Antigen mutation: | No |
| Durg Target: | |
Sequence information
Antibody
Heavy Chain: C
Mutation: NULL
| >6V8X_C|Chain C, G, K|VRC01 Fab Heavy Chain|Homo sapiens (9606) QVQLVQSGGQMKKPGESMRISCRASGYEFIDCTLNWIRLAPGKRPEWMGWLKPRGGAVNYARPLQGRVTMTRDVYSDTAFLELRSLTVDDTAVYFCTRGKNCDYNWDFEHWGRGTPVIVSSPSTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKAEPKSC |
Light Chain: D
Mutation: NULL
| >6V8X_D|Chain D, H, L|VRC01 Fab Light Chain|Homo sapiens (9606) VLTQSPGTLSLSPGETAIISCRTSQYGSLAWYQQRPGQAPRLVIYSGSTRAAGIPDRFSGSRWGPDYNLTISNLESGDFGVYYCQQYEFFGQGTKVQVDIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLRSPVTKSFNRGEC |
Antigen
Chain: A
Mutation: NULL
| >6V8X_A|Chain A, E, I|Envelope glycoprotein gp120|Human immunodeficiency virus 1 (11676) NLWVTVYYGVPVWKDAETTLFCASDAKAYETEKHNIWATHACVPTDPNPQEIHLENVTEEFNMWKNNMVEQMHTDIISLWDQSLKPCVKLTPLCVTLQCTNVTNAITDDMRGELKNCSFNMTTELRDKKQKVYSLFYRLDVVQINENQGNRSNNSNKEYRLINCNTSAITQVCPKLSFEPIPIHYCAPAGFAILKCKDKKFNGTGPCPSVSTVQCTHGIKPVLSTQLLLNGSLAEEEVMIRSENITNNAKNILVQFNTPVQINCTRPNNNTRKSIRIGPGQAFYATGDIIGDIRQAHCNVSKATWNETLGKVVKQLRKHFGNNTIIRFANSSGGDLEVTTHSFNCGGEFFYCNTSGLFNSTWISNTSVQGSNSTGSNDSITLPCRIKQIINMWQRIGQAMYAPPIQGVIRCVSNITGLILTRDGGSTNSTTETFRPGGGDMRDNWRSELYKYKVVKIEPLGVAPTRCKRRV |
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)
| C: ILE30 THR33 TRP47 TRP50 ARG53 GLY54 GLY55 ALA56 VAL57 ASN58 TYR59 ALA60 ARG61 PRO62 GLN64 ARG71 VAL73 TYR74 ASP99 D: VAL3 GLN27 TYR30 TYR91 GLU96 PHE97 A: THR198 ASN276 THR278 ASN279 ASN280 ALA281 LYS282 ASN283 SER365 GLY366 GLY367 ASP368 VAL371 TRP427 GLN428 ARG429 ILE430 GLY431 THR455 ARG456 ASP457 GLY458 GLY459 SER460 THR461 ASN462 THR465 GLU466 THR467 ARG469 GLY472 GLY473 |
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)
