Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 1884 |
| PDBID: | 5W4L |
| Chains: | FI_A |
| Organism: | Human immunodeficiency virus 1, synthetic construct, Homo sapiens |
| Method: | XRD |
| Resolution (Å): | 2.92 |
| Reference: | 10.1016/j.str.2017.09.009 |
| Antibody | |
| Antibody: | N5-i5 Fab |
| Antibody mutation: | No |
| INN (Clinical Trial): | |
| Antigen | |
| Antigen: | HIV-1 clade A/E 93TH05 gp120 |
| Antigen mutation: | Yes |
| Durg Target: | |
Sequence information
Antibody
Heavy Chain: F
Mutation: NULL
| >5W4L_F|Chain C[auth F], I[auth H]|Antibody N5-i5 Fab heavy chain|Homo sapiens (9606) EVQLVESGGGLVQPGGSLRLSCAASGFTFSTYAMSWVRQAPGKGLEWVSSINNSGRNTFSADSVKGRFTISRDNSKNTLFLVMNSLRAEDTAVYYCAKDLRLGGGSDYWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSCDKTH |
Light Chain: I
Mutation: NULL
| >5W4L_I|Chain D[auth I], J[auth L]|Antibody N5-i5 light chain|Homo sapiens (9606) QSALTQPASVSGSPGQSITISCTGTSSDVGSYNFVSWYQQHPGKAPKLMIYEVSERPSGISNRFSGSKSGNTASLTISGLQAEDEADYYCSSYAGSTTFRVFGGGTKLTVRGQPKAAPSVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSYLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPTECS |
Antigen
Chain: A
Mutation: H255S
| >5W4L_A|Chain A, G|clade A/E 93TH057 HIV-1 gp120 core|Human immunodeficiency virus 1 (11676) SDNLWVTVYYGVPVWKDADTTLFCASDAKAHETEVHNVWATHACVPTDPNPQEIHLENVTENFNMWKNNMVEQMQEDVISLWDQSLQPCVKLTGGSVIKQACPKISFDPIPIHYCTPAGYVILKCNDKNFNGTGPCKNVSSVQCTHGIKPVVSTQLLLNGSLAEEEIIIRSENLTNNAKTIIVHLNKSVEINCTRPSNGGSGSGGDIRKAYCEINGTKWNKVLKQVTEKLKEHFNNKTIIFQPPSGGDLEITMHSFNCRGEFFYCNTTQLFNNTCIGNETMKGCNGTITLPCKIKQIINMWQGTGQAMYAPPIDGKINCVSNITGILLTRDGGANNTSNETFRPGGGNIKDNWRSELYKYKVVQIEPLGIAPTKAKRRVVQREKR |
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 F: SER30 THR31 TYR32 ALA33 ASN52 SER53 ARG55 ASN56 PHE58 LYS64 LEU96 ARG97 LEU98 I: SER29 TYR30 PHE32 GLU50 GLU53 TYR91 GLY93 SER94 PHE95 A: THR51 LEU52 PHE53 CYS54 SER56 ALA58 ALA60 HIS61 VAL68 TRP69 THR71 HIS72 ALA73 CYS74 VAL75 PRO76 THR77 ASP78 PRO79 ASN80 GLN103 GLU106 ASP107 SER110 GLN114 ALA221 |
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)
