Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 939 |
| PDBID: | 4RFN |
| Chains: | BC_A |
| Organism: | Human immunodeficiency virus 1, Macaca mulatta, synthetic construct |
| Method: | XRD |
| Resolution (Å): | 3.21 |
| Reference: | 10.1128/JVI.01232-15 |
| Antibody | |
| Antibody: | JR4 Fab |
| Antibody mutation: | No |
| INN (Clinical Trial): | |
| Antigen | |
| Antigen: | HIV-1 clade A/E 93TH057 (H375S) gp120 |
| Antigen mutation: | No |
| Durg Target: | |
Sequence information
Antibody
Heavy Chain: B
Mutation: NULL
| >4RFN_B|Chain B, F[auth H]|FAB HEAVY CHAIN OF ADCC ANTI-HIV-1 ANTIBODY JR4|Macaca mulatta (9544) HSEVQLVESGPGLVKPLETLSLTCAVPGGSIRRNYWSWIRQPPGKGLEWIGHSYGSGGSTNYNPSLESRVTLSVDTSKNLFSLKLTSVTAADTAVYYCARTVWYYTSGTHYFDHWGQGVLVTVSSASTKGPSVFPLAPSSRSTSESTAALGCLVKDYFPEPVTVSWNSGSLTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYVCNVNHKPSNTKVDKRVEIKTCGGGSK |
Light Chain: C
Mutation: NULL
| >4RFN_C|Chain C, G[auth L]|FAB LIGHT CHAIN OF ADCC ANTI-HIV-1 ANTIBODY JR4|Macaca mulatta (9544) QSVLTQPPSVSAAPGQKVTISCSGSSSNIGRSYVSWYQQVPGAAPKLLIYDTNKRPSGVSDRFSGSKSGSSASLAITGLQTGDEADYYCGAWDGSLNVHIFGSGTKLTVLGQPKASPLVTLFPPSSEELQANKATLVCLISDFYPGVVKVAWKADGNSVNTGVETTTPSKQSNNKYAASSYLSLTSDQWKSHKSYSCQVTHEGSTVEKTVAPTECS |
Antigen
Chain: A
Mutation: NULL
| >4RFN_A|Chain A, E[auth G]|HIV-1 CLADE A/E 93TH057 (H375S) GP120|Human immunodeficiency virus 1 (11676) VWKDADTTLFCASDAKAHETEVHNVWATHACVPTDPNPQEIHLENVTENFNMWKNNMVEQMQEDVISLWDQSLQPCVKLTGGSVIKQACPKISFDPIPIHYCTPAGYVILKCNDKNFNGTGPCKNVSSVQCTHGIKPVVSTQLLLNGSLAEEEIIIRSENLTNNAKTIIVHLNKSVEINCTRPSNGGSGSGGDIRKAYCEINGTKWNKVLKQVTEKLKEHFNNKTIIFQPPSGGDLEITMHSFNCRGEFFYCNTTQLFNNTCIGNETMKGCNGTITLPCKIKQIINMWQGTGQAMYAPPIDGKINCVSNITGILLTRDGGANNTSNETFRPGGGNIKDNWRSELYKYKVVQIE |
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)
| B: GLU1 VAL2 GLN3 GLY26 SER28 ARG30 ARG31 ASN32 TYR33 SER53 GLY54 GLY55 SER56 ASN58 ARG94 THR95 VAL96 TRP97 TYR98 TYR99 ASP101 HIS102 C: TYR32 TYR49 ASP50 LYS53 SER56 GLY57 A: THR50 THR51 LEU52 PHE53 CYS54 ALA55 LYS59 ALA60 HIS61 TRP69 THR71 HIS72 ALA73 CYS74 VAL75 PRO76 THR77 ASP78 PRO79 ASN80 GLN82 ILE84 GLN103 GLU106 ASP107 TYR217 PRO220 ALA221 GLY222 TYR223 GLN246 CYS247 GLU492 |
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)
