Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 4150 |
| PDBID: | 7LL1 |
| Chains: | EF_C |
| Organism: | Human immunodeficiency virus 1, Homo sapiens |
| Method: | EM |
| Resolution (Å): | 3.73 |
| Reference: | 10.1016/j.celrep.2021.109922 |
| Antibody | |
| Antibody: | VRC40.01 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
| >7LL1_E|Chain G[auth E], I[auth H], K[auth J]|VRC40.01 Fab Heavy chain|Homo sapiens (9606) QVQLIQSGPQFKTPGASVTVSCKASGYIFTDYLIHWVRLVPGKGLEWLGRINTNAGLMYLSHKFEGRLILRRVVDWRTPSLGTVNMELRNVRSDDSAIYFCGRVVDGFNAAGPLEFWGQGSPVIVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKS |
Light Chain: F
Mutation: NULL
| >7LL1_F|Chain H[auth F], J[auth K], L|VRC40.01 Fab Light chain|Homo sapiens (9606) QVVMTQSPATLSLSPGETAAVSCRASQYVDRSISWYQLKTGRAPRLLVYAASSRSIGVPDRFSGSGSGRDFTLTIRGVQSDDFALYYCQQDYYWPVTFGQGTRLDMKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC |
Antigen
Chain: C
Mutation: NULL
| >7LL1_C|Chain A, C, E[auth G]|Envelope glycoprotein gp120|Human immunodeficiency virus 1 (11676) AENLWVTVYYGVPVWKDAETTLFCASDAKAYETEKHNVWATHACVPTDPNPQEIHLENVTEEFNMWKNNMVEQMHTDIISLWDQSLKPCVKLTPLCVTLQCTNVTNNITDDMRGELKNCSFNMTTELRDKKQKVYSLFYRLDVVQINENQGNRSNNSNKEYRLINCNTSACTQACPKVSFEPIPIHYCAPAGFAILKCKDKKFNGTGPCPSVSTVQCTHGIKPVVSTQLLLNGSLAEEEVMIRSENITNNAKNILVQFNTPVQINCTRPNNNTRKSIRIGPGQAFYATGDIIGDIRQAHCNVSKATWNETLGKVVKQLRKHFGNNTIIRFANSSGGDLEVTTHSFNCGGEFFYCNTSGLFNSTWISNTSVQGSNSTGSNDSITLPCRIKQIINMWQRIGQCMYAPPIQGVIRCVSNITGLILTRDGGSTNSTTETFRPGGGDMRDNWRSELYKYKVVKIEPLGVAPTRCKRRV |
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)
| Chain residues position delta_SASA
: residuesposition E: THR30 ASP31 TYR32 LEU33 ARG50 ASN53 ALA54 GLY55 LEU56 MET57 TYR58 ILE68 LEU69 ARG70 ARG71 GLY98 F: TYR28 TYR92 TYR93 TRP94 C: GLU102 HIS105 THR106 ILE109 THR278 ASN279 ASN280 ALA281 LYS282 ASN283 SER364 SER365 GLY366 GLY367 ASP368 VAL371 TRP427 GLN428 ARG429 ILE430 THR455 ARG456 ASP457 GLY458 GLY459 SER460 THR461 ASN462 ARG469 PRO470 GLY471 GLY472 GLY473 ASP474 ARG476 |
2、We defined interacting paratope-epitope residues by a distance cutoff of < 6 Å . Two amino acids are considered as interacting residues if they have at least one atom within a distance of 6 Å from any atom.
Interacting residues (Atom distance based)
