Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 1047 |
| PDBID: | 4XMP |
| Chains: | HL_G |
| Organism: | Human immunodeficiency virus 1, Homo sapiens |
| Method: | XRD |
| Resolution (Å): | 1.78 |
| Reference: | 10.1016/j.cell.2015.03.004 |
| Antibody | |
| Antibody: | VRC08 Fab |
| Antibody mutation: | No |
| INN (Clinical Trial): | |
| Antigen | |
| Antigen: | HIV-1 clade A strain Q842.d12 gp120 |
| Antigen mutation: | No |
| Durg Target: | P35961 |
Sequence information
Antibody
Heavy Chain: H
Mutation: NULL
| >4XMP_H|Chain B[auth H]|HEAVY CHAIN OF ANTIBODY VRC08|Homo sapiens (9606) QVQLVQSGTQMKEPGASVTISCVTSGYEFVEILINWVRQVPGRGLEWMGWMNPRGGGVNYARQFQGKVTMTRDVYRDTAYLTLSGLTSGDTAKYFCVRGRSCCGGRRHCNGADCFNWDFQHWGQGTLVIVSPASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSC |
Light Chain: L
Mutation: NULL
| >4XMP_L|Chain C[auth L]|LIGHT CHAIN OF ANTIBODY VRC08|Homo sapiens (9606) YIGVTQSPAILSVSLGERVTLSCKTSQAITPRHLVWHRQKGGQAPSLVMTGTSERASGIPDRFIGSGSGTDFTLTITRLEAEDFAVYYCQCLEAFGQGTKLEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC |
Antigen
Chain: G
Mutation: NULL
| >4XMP_G|Chain A[auth G]|Envelope glycoprotein gp160,Envelope glycoprotein gp160,Envelope glycoprotein gp160|Human immunodeficiency virus 1 (11676) VWKEAETTLFCASDAKAYETEKHNVWATHACVPTDPNPQEIHLENVTEEFNMWKNNMVEQMHTDIISLWDQSLKPCVKLTGGSAITQACPKVTFEPIPIHYCAPAGFAILKCKDEEFNGIGPCKNVSTVQCTHGIKPVVSTQLLLNGSLAEKEVKIRCENITNNAKTIIVQLVNPVKINCTRPNNGGSGSGGDIRQAHCNVNRTEWNNTLHQVVEQLRKHFNKTINFANSTGGDLEITTHSFNCGGEFFYCNTTNLFNSTWNHTASMNSTESNDTIILPCRIKQIINMWQRVGQAMYAPPIRGVIRCESNITGLILTRDGGNTNSTRETFRPGGGDMRDNWRSELYKYKVVKIE |
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 H: VAL30 LEU33 TRP47 TRP50 ARG53 GLY54 GLY55 GLY56 VAL57 ASN58 TYR59 ALA60 ARG61 GLN62 GLN64 ARG71 VAL73 TYR74 L: TYR1 ILE2 ARG31 HIS32 LEU91 GLU96 G: GLU49 LYS97 ASN99 GLU102 GLN103 HIS105 THR106 ILE109 GLY124 GLY198 GLU275 ASN276 THR278 ASN279 ASN280 ALA281 LYS282 THR283 PHE353 LYS357 THR365 GLY366 GLY367 ASP368 ILE371 MET426 TRP427 ARG429 VAL430 THR455 ARG456 ASP457 GLY458 GLY459 ASN460 THR461 ARG465 GLU466 THR467 ARG469 ASP474 ARG476 ARG480 |
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)
