Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 6874 |
| PDBID: | 4I3S |
| Chains: | HL_G |
| Organism: | Human immunodeficiency virus, Homo sapiens |
| Method: | XRD |
| Resolution (Å): | 2.85 |
| Reference: | 10.1128/JVI.02717-12 |
| Antibody | |
| Antibody: | VRC-PG04 Fab |
| Antibody mutation: | No |
| INN (Clinical Trial): | |
| Antigen | |
| Antigen: | The outer domain of the HIV-1 envelope glycoprotein gp120 |
| Antigen mutation: | No |
| Durg Target: | |
Sequence information
Antibody
Heavy Chain: H
Mutation: NULL
| >4I3S_H|Chain B[auth H]|Heavy chain of VRC-PG04 Fab|Homo sapiens (9606) QVQLVQSGSGVKKPGASVRVSCWTSEDIFERTELIHWVRQAPGQGLEWIGWVKTVTGAVNFGSPDFRQRVSLTRDRDLFTAHMDIRGLTQGDTATYFCARQKFYTGGQGWYFDLWGRGTLIVVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSC |
Light Chain: L
Mutation: NULL
| >4I3S_L|Chain C[auth L]|Light chain of VRC-PG04 Fab|Homo sapiens (9606) EIVLTQSPGTLSLSPGETASLSCTAASYGHMTWYQKKPGQPPKLLIFATSKRASGIPDRFSGSQFGKQYTLTITRMEPEDFARYYCQQLEFFGQGTRLEIRRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC |
Antigen
Chain: G
Mutation: NULL
| >4I3S_G|Chain A[auth G]|Outer domain of HIV-1 gp120 (KER2018 OD4.2.2)|Human Immunodeficiency Virus (12721) KPVVSTQLLLNGSLAEKEIRIKSEDISDNAKNIIVQLTKPVLINCARPSNNTQYCVVNRTQWNDTLGQVAIQLRKHWNTCIIFNEPSGGDLEITTHSFNCGGEFFYCNTSDLFNSTWNIEGTASIDGTESNDDITLPCRIKGSGAPPIQGVIRCQSNITGILLTRDGGSGSGTCETFRPGGGDMRDNWRS |
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 TYR98 THR99 L: GLU1 ILE2 LEU91 GLU96 PHE97 G: LYS252 PRO253 VAL254 SER256 GLU275 ASP276 SER278 ASP279 ASN280 ALA281 LYS282 ASN283 SER365 GLY366 GLY367 ASP368 ILE371 THR455 ARG456 ASP457 GLY458 GLY459 SER460 GLY461 SER462 ARG469 GLY472 GLY473 ASP474 |
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)
