Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 1109 |
| PDBID: | 4YDK |
| Chains: | HL_G |
| Organism: | Human immunodeficiency virus 1, Homo sapiens |
| Method: | XRD |
| Resolution (Å): | 2.05 |
| Reference: | 10.1016/j.cell.2015.05.007 |
| Antibody | |
| Antibody: | C38-VRC16.01 Fab |
| Antibody mutation: | No |
| INN (Clinical Trial): | |
| Antigen | |
| Antigen: | HIV-1 clade AE strain 93TH057 gp120 |
| Antigen mutation: | No |
| Durg Target: | |
Sequence information
Antibody
Heavy Chain: H
Mutation: NULL
| >4YDK_H|Chain B[auth H]|HEAVY CHAIN OF ANTIBODY C38-VRC16.01|Homo sapiens (9606) EVQLSESGGGFVKPGGSLRLSCEASGFTFNNYAMGWVRQAPGKGLEWVSVTSAHGGSAYFGEFVKGRFTMSRDHFIDTVYLEMNRLTVEDTAVYYCVRVTFYHEGSGYYYRAGNYFDSWGQGTLVIVSAASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDK |
Light Chain: L
Mutation: NULL
| >4YDK_L|Chain C[auth L]|LIGHT CHAIN OF ANTIBODY C38-VRC16.01|Homo sapiens (9606) DIQMTQSPSSLSASIGDRVTITCRASQDIANYLNWYQKKSGTPPKLLIFGATNLHHGVSPRFSGSGHGTHFSLTITNVQHEDFANYFCQQSFQTVGSFGQGTWVDIRRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC |
Antigen
Chain: G
Mutation: NULL
| >4YDK_G|Chain A[auth G]|Envelope glycoprotein gp160,Envelope glycoprotein gp160|Human immunodeficiency virus 1 (11676) VWKDADTTLFCASDAKAHETEVHNVWATHACVPTDPNPQEIHLENVTENFNMWKNNMVEQMQEDVISLWDQSLQPCVKLTGGSVIKQACPKISFDPIPIHYCTPAGYVILKCNDKNFNGTGPCKNVSSVQCTHGIKPVVSTQLLLNGSLAEEEIIIRSENLTNNAKTIIVHLNKSVEINCTRPSNGGSGSGGDIRKAYCEINGTKWNKVLKQVTEKLKEHFNNKTIIFQPPSGGDLEITMHHFNCRGEFFYCNTTQLFNNTCIGNETMKGCNGTITLPCKIKQIINMWQGTGQAMYAPPIDGKINCVSNITGILLTRDGGANNTSNETFRPGGGNIKDNWRSELYKYKVVQIE |
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)
| H: HIS53 GLY54 GLY55 SER56 TYR58 SER70 ARG71 ASP72 HIS73 PHE74 TYR98 HIS99 L: ALA30 ASN31 TYR32 THR52 ASN53 HIS67 PHE92 GLN93 THR94 G: GLN105 THR123 GLY124 GLY198 SER199 THR257 GLU275 ASN280 ALA281 LYS282 THR283 PRO364 SER365 GLY366 GLY367 ASP368 GLU370 ILE371 HIS375 ASN425 MET426 TRP427 GLN428 GLY429 GLY431 GLN432 THR455 ARG456 ASP457 GLY458 GLY459 ALA460 THR463 ARG469 PRO470 GLY471 GLY472 GLY473 ASN474 ASP477 |
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)
