Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 3060 |
| PDBID: | 6VY2 |
| Chains: | IM_C |
| Organism: | Human immunodeficiency virus 1, Homo sapiens |
| Method: | EM |
| Resolution (Å): | 4.86 |
| Reference: | 10.1016/j.chom.2020.03.024 |
| Antibody | |
| Antibody: | M1214_N1 Fab |
| Antibody mutation: | No |
| INN (Clinical Trial): | |
| Antigen | |
| Antigen: | HIV-1 CH505 SOSIP.664 gp120 |
| Antigen mutation: | No |
| Durg Target: | |
Sequence information
Antibody
Heavy Chain: I
Mutation: NULL
| >6VY2_I|Chain G[auth H], H[auth I], I[auth J]|M1214 N1 Fab heavy chain|Homo sapiens (9606) DRLFQSGGGVSRPGGSLRVNCGASGFTVRTHYMYWLRQSPGKGLEWVAFMNSGGSVSYVDSVRGRFSVSRDNPANAMVLQMDALKIEDTGTYYCARELREAWYGDLRDYSGLDVWGRGTIVSISSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPK |
Light Chain: M
Mutation: NULL
| >6VY2_M|Chain J[auth L], K[auth M], L[auth N]|M1214 N1 Fab light chain|Homo sapiens (9606) QSALAQPPSVSGSPGQSVTITCTGINDYGAAYKFVSWYQQHPGKEPRLIMKNVKDRWSVTPNRFSGSTSGNTASLTISNLQSDDEAQYFCAVYAGGFTFPRLGGGTKLSVLSQPKAAPSVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSYLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPT |
Antigen
Chain: C
Mutation: NULL
| >6VY2_C|Chain A, C, E|Glycoprotein 120|Human immunodeficiency virus 1 (11676) MPMGSLQPLATLYLLGMLVASVLAAENLWVTVYYGVPVWKEAKTTLFCASDAKAYEKKVHNVWATHACVPTDPNPQEMVLKNVTENFNMWKNDMVDQMHEDVISLWDQSLKPCVKLTPLCVTLNCTNATASNSSIIEGMKNCSFNITTELRDKREKKNALFYKLDIVQLDGNSSQYRLINCNTSVITQACPKVSFDPIPIHYCAPAGYAILKCNNKTFTGTGPCNNVSTVQCTHGIKPVVSTQLLLNGSLAEGEIIIRSENITNNVKTIIVHLNESVKIECTRPNNKTRTSIRIGPGQWFYATGQVIGDIREAYCNINESKWNETLQRVSKKLKEYFPHKNITFQPSSGGDLEITTHSFNCGGEFFYCNTSSLFNRTYMANSTDMANSTETNSTRTITIHCRIKQIINMWQEVGRAMYAPPIAGNITCISNITGLLLTRDGGKNNTETFRPGGGNMKDNWRSELYKYKVVKIEPLGVAPTRCKRRVV |
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)
| I: SER25 GLY26 PHE27 THR28 ARG30 THR31 HIS32 TYR33 SER53 ASN73 PRO74 ALA75 ASN76 LEU96 ARG97 GLU98 ALA99 M: ALA28 ALA29 TYR30 C: LYS178 LEU179 ILE181 VAL182 GLN183 LEU184 ASP185 GLY186 ILE194 ASN195 ASN197 THR198 ASN280 VAL281 GLN362 SER365 GLY366 GLY367 ASP368 LEU369 GLU370 ILE371 TYR384 LYS421 ILE423 ILE424 ASN425 MET426 TRP427 THR455 ARG456 ASP457 GLY458 GLY459 LYS460 ARG469 |
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)
