Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 2655 |
| PDBID: | 6OT1 |
| Chains: | qr_G |
| Organism: | Human immunodeficiency virus 1, Macaca mulatta, Homo sapiens |
| Method: | EM |
| Resolution (Å): | 3.50 |
| Reference: | 10.1016/j.cell.2019.06.030 |
| Antibody | |
| Antibody: | VRC03 Fab |
| Antibody mutation: | No |
| INN (Clinical Trial): | |
| Antigen | |
| Antigen: | HIV-1 BG505 DS-SOSIP gp120 |
| Antigen mutation: | No |
| Durg Target: | |
Sequence information
Antibody
Heavy Chain: q
Mutation: NULL
| >6OT1_q|Chain G[auth J], O[auth S], W[auth q]|VRC03 heavy|Homo sapiens (9606) QVQLVQSGAVIKTPGSSVKISCRASGYNFRDYSIHWVRLIPDKGFEWIGWIKPLWGAVSYARQLQGRVSMTRQLSQDPDDPDWGVAYMEFSGLTPADTAEYFCVRRGSCDYCGDFPWQYWGQGTVVVVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSC |
Light Chain: r
Mutation: NULL
| >6OT1_r|Chain H[auth K], P[auth T], X[auth r]|VRC03 light|Homo sapiens (9606) EIVLTQSPGILSLSPGETATLFCKASQGGNAMTWYQKRRGQVPRLLIYDTSRRASGVPDRFVGSGSGTDFFLTINKLDREDFAVYYCQQFEFFGLGSELEVHRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC |
Antigen
Chain: G
Mutation: NULL
| >6OT1_G|Chain B[auth E], J[auth G], R[auth P]|BG505 gp120|Human immunodeficiency virus 1 (11676) AENLWVTVYYGVPVWKDAETTLFCASDAKAYETEKHNVWATHACVPTDPNPQEIHLENVTEEFNMWKNNMVEQMHTDIISLWDQSLKPCVKLTPLCVTLQCTNVTNNITDDMRGELKNCSFNMTTELRDKKQKVYSLFYRLDVVQINENQGNRSNNSNKEYRLINCNTSACTQACPKVSFEPIPIHYCAPAGFAILKCKDKKFNGTGPCPSVSTVQCTHGIKPVVSTQLLLNGSLAEEEVMIRSENITNNAKNILVQFNTPVQINCTRPNNNTRKSIRIGPGQAFYATGDIIGDIRQAHCNVSKATWNETLGKVVKQLRKHFGNNTIIRFANSSGGDLEVTTHSFNCGGEFFYCNTSGLFNSTWISNTSVQGSNSTGSNDSITLPCRIKQIINMWQRIGQCMYAPPIQGVIRCVSNITGLILTRDGGSTNSTTETFRPGGGDMRDNWRSELYKYKVVKIEPLGVAPTRCKRRVGRRRRRR |
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)
| q: ARG30 SER33 HIS35 GLU46 TRP47 TRP50 LYS52 LEU54 TRP55 GLY56 ALA57 VAL58 SER59 TYR60 ALA61 ARG62 GLN63 GLN65 MET70 ARG72 LEU74 SER75 GLN76 ASP77 PRO78 PRO81 ASP110 TYR111 CYS112 GLY113 ASP114 PHE115 r: GLU1 ILE2 GLN27 ASN30 PHE90 GLU91 PHE92 G: LYS67 THR168 THR227 ASN246 THR248 ASN249 ASN250 ALA251 LYS252 ASN253 SER334 GLY335 GLY336 ASP337 GLU339 VAL340 MET394 TRP395 GLN396 ARG397 ILE398 GLY399 THR423 ARG424 ASP425 GLY426 GLY427 SER428 THR429 ASN430 SER431 THR433 GLU434 THR435 ARG437 GLY439 GLY441 ASP442 MET443 |
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)
