Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 3906 |
| PDBID: | 7KDE |
| Chains: | MN_E |
| Organism: | Human immunodeficiency virus 1, Homo sapiens |
| Method: | EM |
| Resolution (Å): | 3.55 |
| Reference: | 10.7554/eLife.61991 |
| Antibody | |
| Antibody: | Ab1485 Fab |
| Antibody mutation: | No |
| INN (Clinical Trial): | |
| Antigen | |
| Antigen: | HIV-1 BG505 SOSIP.664 gp120 |
| Antigen mutation: | No |
| Durg Target: | |
Sequence information
Antibody
Heavy Chain: M
Mutation: NULL
| >7KDE_M|Chain G[auth H], H[auth J], I[auth M]|Ab 1485 Heavy Chain|Homo sapiens (9606) EVQLVESGPGLVKASETLSLTCTVSGYNIRSNNWWSWVRQPPGKGLEWIGGVYANSEITNYNSSLKSRVSISQDAWRNKFSLKLKSVTDADTAVYYCVRGPNHWEYFDSGNNEYFEFWGQGALVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSCDK |
Light Chain: N
Mutation: NULL
| >7KDE_N|Chain P[auth I], Q[auth L], R[auth N]|Ab 1485 Light Chain|Homo sapiens (9606) QSALTQPPSVSGAPGQRVTISCTGTSSNIENYHAFWYQQFSGMAPKLLIRDNDKRPSGVSDRFSGSKSGASASLTITGLQTDDEADYYCQSYDSGLRSYIFASGTRLTVLGQPKASPTVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSYLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPTECS |
Antigen
Chain: E
Mutation: NULL
| >7KDE_E|Chain D[auth E], E[auth F], F[auth G]|Envelope glycoprotein gp120|Human immunodeficiency virus 1 (11676) NLWVTVYYGVPVWKDAETTLFCASDAKAYETEKHNVWATHACVPTDPNPQEIHLENVTEEFNMWKNNMVEQMHTDIISLWDQSLKPCVKLTPLCVTLQCTNVTNNITDDMRGELKNCSFNMTTELRDKKQKVYSLFYRLDVVQINENQGNRSNNSNKEYRLINCNTSAITQACPKVSFEPIPIHYCAPAGFAILKCKDKKFNGTGPCPSVSTVQCTHGIKPVVSTQLLLNGSLAEEEVMIRSENITNNAKNILVQFNTPVQINCTRPNNNTRKSIRIGPGQAFYATGDIIGDIRQAHCNVSKATWNETLGKVVKQLRKHFGNNTIIRFANSSGGDLEVTTHSFNCGGEFFYCNTSGLFNSTWISNTSVQGSNSTGSNDSITLPCRIKQIINMWQRIGQAMYAPPIQGVIRCVSNITGLILTRDGGSTNSTTETFRPGGGDMRDNWRSELYKYKVVKIEPLGVAPTRCKRRVVGRRRRRR |
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 M: TYR27 ASN28 ARG30 SER31 ASN32 ALA52 ASN53 SER54 GLU55 ALA73 TRP74 ASN97 HIS98 TRP99 E: VAL134 THR135 ASN156 PRO299 ASN300 ASN301 ASP321 ILE322 ILE323 GLY324 ASP325 ILE326 ARG327 VAL442 |
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)
