Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 2563 |
| PDBID: | 6NNF |
| Chains: | UV_G |
| Organism: | Human immunodeficiency virus 1, Homo sapiens |
| Method: | XRD |
| Resolution (Å): | 2.76 |
| Reference: | 10.1038/s41467-019-08658-4 |
| Antibody | |
| Antibody: | VRC01 FR3-03 Fv |
| Antibody mutation: | No |
| INN (Clinical Trial): | |
| Antigen | |
| Antigen: | HIV-1 BG505 SOSIP.664 gp120 |
| Antigen mutation: | Yes |
| Durg Target: | |
Sequence information
Antibody
Heavy Chain: U
Mutation: NULL
| >6NNF_U|Chain G[auth U]|VRC01 FR3-03 heavy chain|Homo sapiens (9606) QVQLVQSGGQMKKPGESMRISCRASGYEFIDCTLNWIRLAPGKRPEWMGWLKPRGGAVNYARPLQGRVTMTRQLSQDPDDPDWGTAFLELRSLTVDDTAVYFCTRGKNCDYNWDFEHWGRGTPVIVGGLVPRGSHHHHHHHH |
Light Chain: V
Mutation: NULL
| >6NNF_V|Chain H[auth V]|VRC01 FR3-03 light chain|Homo sapiens (9606) EIVLTQSPGTLSLSPGETAIISCRTSQYGSLAWYQQRPGQAPRLVIYSGSTRAAGIPDRFSGSRWGPDYNLTISNLESGDFGVYYCQQYEFFGQGTKVQVGGGGSGGGGSGGGGS |
Antigen
Chain: G
Mutation: N107A/T301A/A469C
| >6NNF_G|Chain D[auth G]|Envelope glycoprotein gp120|Human immunodeficiency virus 1 (11676) AENLWVTVYYGVPVWKDAETTLFCASDAKAYETEKHNVWATHACVPTDPNPQEIHLENVTEEFNMWKNNMVEQMHTDIISLWDQSLKPCVKLTPLCVTLQCTNVTNAITDDMRGELKNCSFNMTTELRDKKQKVYSLFYRLDVVQINENQGNRSNNSNKEYRLINCNTSAITQACPKVSFEPIPIHYCAPAGFAILKCKDKKFNGTGPCPSVSTVQCTHGIKPVVSTQLLLNGSLAEEEVMIRSENITNNAKNILVQFNTPVQINCTRPNNNTRKSIRIGPGQAFYATGDIIGDIRQAHCNVSKATWNETLGKVVKQLRKHFGNNTIIRFANSSGGDLEVTTHSFNCGGEFFYCNTSGLFNSTWISNTSVQGSNSTGSNDSITLPCRIKQIINMWQRIGQAMYAPPIQGVIRCVSNITGLILTRDGGSTNSTTETFRPGGGDMRDNWRSELYKYKVVKIEPLGVAPTRCKRRVVGRRRRRR |
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)
| U: ILE30 THR33 TRP47 TRP50 ARG53 GLY54 GLY55 ALA56 VAL57 ASN58 TYR59 ALA60 ARG61 PRO62 GLN64 MET69 THR70 ARG71 LEU73 SER74 GLN75 ASP99 V: VAL3 GLN27 TYR91 GLU96 PHE97 G: ASN197 THR198 ASN276 THR278 ASN279 ASN280 ALA281 LYS282 ASN283 ARG360 SER365 GLY366 GLY367 ASP368 VAL371 GLN428 ARG429 ILE430 GLY431 THR455 ARG456 ASP457 ASN462 SER463 THR465 GLU466 THR467 ARG469 GLY471 GLY473 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)
