Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 649 |
| PDBID: | 3SE9 |
| Chains: | HL_G |
| Organism: | Human immunodeficiency virus 1, Homo sapiens |
| Method: | XRD |
| Resolution (Å): | 2.00 |
| Reference: | 10.1126/science.1207532 |
| Antibody | |
| Antibody: | VRC-PG04 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
| >3SE9_H|Chain B[auth H]|Heavy chain of antibody VRC-PG04|Homo sapiens (9606) QVQLVQSGSGVKKPGASVRVSCWTSEDIFERTELIHWVRQAPGQGLEWIGWVKTVTGAVNFGSPDFRQRVSLTRDRDLFTAHMDIRGLTQGDTATYFCARQKFYTGGQGWYFDLWGRGTLIVVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSC |
Light Chain: L
Mutation: NULL
| >3SE9_L|Chain C[auth L]|Light chain of antibody VRC-PG04|Homo sapiens (9606) EIVLTQSPGTLSLSPGETASLSCTAASYGHMTWYQKKPGQPPKLLIFATSKRASGIPDRFSGSQFGKQYTLTITRMEPEDFARYYCQQLEFFGQGTRLEIRRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC |
Antigen
Chain: G
Mutation: NULL
| >3SE9_G|Chain A[auth G]|HIV-1 Clade AE strain 93TH057 gp120|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: GLU33 LEU34 TRP47 TRP50 VAL52 THR53 GLY54 ALA55 VAL56 ASN57 PHE58 GLY59 SER60 PRO61 ARG64 ARG71 ARG73 ASP74 TYR98 THR99 L: GLU1 VAL3 SER27 LEU91 GLU96 PHE97 G: LYS97 LEU122 GLY124 GLU275 ASN276 THR278 ASN279 ASN280 ALA281 LYS282 THR283 SER365 GLY366 GLY367 ASP368 ILE371 GLY429 GLY431 THR455 ARG456 ASP457 GLY458 GLY459 ASN461 ASN462 ARG469 GLY472 GLY473 ASN474 LYS476 |
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)
