Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 805 |
| PDBID: | 4LAJ |
| Chains: | L_A |
| Organism: | Human immunodeficiency virus 1, Lama glama |
| Method: | XRD |
| Resolution (Å): | 2.14 |
| Reference: | 10.1128/JVI.01332-13 |
| Antibody | |
| Antibody: | JM4 VHH |
| Antibody mutation: | No |
| INN (Clinical Trial): | |
| Antigen | |
| Antigen: | HIV-1 YU2 gp120 |
| Antigen mutation: | No |
| Durg Target: | P35961 |
Sequence information
Antibody
Chain: L
Mutation: NULL
| >4LAJ_L|Chain I[auth H], J[auth I], K[auth L], L[auth M]|Llama single domain antibody, JM4|Lama glama (9844) EVQLVESGGGLVQPGGSLRLSCAASGFTLDYYSIGWFRQAPGKEREGVSCISDSDGRTYYADSVKGRFTISRDNAKNTVYLQMNSLKPEDTAVYYCATDCTVDPSLLYVMDYYGKGTQVTVSSAAAEQK |
Antigen
Chain: A
Mutation: NULL
| >4LAJ_A|Chain A, B, C[auth F], D[auth J]|HIV-1 YU2 gp120 envelope glycoprotein|Human immunodeficiency virus 1 (11676) MPMGSLQPLATLYLLGMLVASVLAVWKEATTTLFCASDAKAYDTEVHNVWATHACVPTDPNPQEVKLENVTENFNMWKNNMVEQMHEDIISLWDQSLKPCVKLTGGSVITQACPKVSFEPIPIHYCAPAGFAILKCNDKKFNGTGPCTNVSTVQCTHGIRPVVSTQLLLNGSLAEEEIVIRSENFTNNAKTIIVQLNESVVINCTRPNNGGSGSGGDIRQAHCNLSKTQWENTLEQIAIKLKEQFGNNKTIIFNPSSGGDPEIVTHSFNCGGEFFYCNSTQLFTWNDTRKLNNTGRNITLPCRIKQIINMWQEVGKAMYAPPIRGQIRCSSNITGLLLTRDGGKDTNGTEIFRPGGGDMRDNWRSELYKYKVVKIE |
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)
| L: GLU1 VAL2 GLY26 PHE27 TYR31 TYR32 SER33 SER52 ASP53 ARG57 TYR59 THR98 ASP100 CYS101 THR102 ASP104 SER106 LEU107 TYR109 VAL110 ASP112 TYR113 A: CYS119 VAL120 LEU122 VAL200 ASN301 GLY324 ASP325 ILE326 ARG327 GLN328 GLY367 ASP368 PRO369 VAL372 THR373 TYR384 ASN386 PRO417 CYS418 ARG419 LYS421 GLN422 ILE423 ASN425 LYS432 MET434 TYR435 ALA436 PRO437 ARG440 |
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)
