Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 954 |
| PDBID: | 4S1Q |
| Chains: | HL_G |
| Organism: | Human immunodeficiency virus 1, Homo sapiens |
| Method: | XRD |
| Resolution (Å): | 2.40 |
| Reference: | 10.1016/j.cell.2015.03.004 |
| Antibody | |
| Antibody: | 45-VRC01.H03+06.D-001739 Fab |
| Antibody mutation: | No |
| INN (Clinical Trial): | |
| Antigen | |
| Antigen: | HIV-1 clade A/E gp120 |
| Antigen mutation: | No |
| Durg Target: | |
Sequence information
Antibody
Heavy Chain: H
Mutation: NULL
| >4S1Q_H|Chain B[auth H]|Fab of VRC01-lineage antibody,45-VRC01.H03+06.D-001739 heavy chain|Homo sapiens (9606) EVRLIQSGAVMRKPGSSVKISCRASGYNFREYSIHWVRLIPGRGLEWIGWIKGMWGAVSYARQLQGRVSMTRQLSQDPDDPDWGIAYLEFSGLTSGDTAEYFCVRKGPSCPHCGDFHWQHWGQGTAVVVSAASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSC |
Light Chain: L
Mutation: NULL
| >4S1Q_L|Chain C[auth L]|Fab of VRC01 light chain|Homo sapiens (9606) EIVLTQSPGTLSLSPGETAIISCRTSQYGSLAWYQQRPGQAPRLVIYSGSTRAAGIPDRFSGSRWGPDYTLTISNLESGDFGVYYCQQYEFFGQGTKVQVDIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC |
Antigen
Chain: G
Mutation: NULL
| >4S1Q_G|Chain A[auth G]|HIV-1 gp120 core|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: ARG30 HIS35 TRP47 TRP50 MET53 TRP54 GLY55 ALA56 VAL57 SER58 TYR59 ALA60 ARG61 GLN62 GLN64 MET69 ARG71 GLN75 PRO99 L: GLU1 ILE2 GLN27 TYR91 GLU96 PHE97 G: LYS97 LEU122 THR123 GLY124 GLY198 THR257 ASN276 THR278 ASN279 ASN280 ALA281 LYS282 THR283 LYS357 SER365 GLY366 GLY367 ASP368 GLU370 ILE371 HIS375 ASN425 MET426 TRP427 GLN428 GLY429 THR430 GLY431 GLN432 THR455 ARG456 ASP457 GLY458 GLY459 ALA460 ASN461 ASN462 THR463 ASN465 GLU466 THR467 ARG469 GLY472 GLY473 ASN474 ILE475 |
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)
