Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 2985 |
| PDBID: | 6V8Z |
| Chains: | CF_A |
| Organism: | Human immunodeficiency virus 1, Homo sapiens |
| Method: | EM |
| Resolution (Å): | 2.90 |
| Reference: | 10.1038/s41467-019-14196-w |
| Antibody | |
| Antibody: | VRC03 Fab |
| Antibody mutation: | No |
| INN (Clinical Trial): | |
| Antigen | |
| Antigen: | HIV-1 BG505 F14 SOSIP gp120 |
| Antigen mutation: | No |
| Durg Target: | |
Sequence information
Antibody
Heavy Chain: C
Mutation: NULL
| >6V8Z_C|Chain E[auth C], K[auth I], Q[auth O]|VRC03 Fab Heavy Chain|Homo sapiens (9606) QVQLVQSGAVIKTPGSSVKISCRASGYNFRDYSIHWVRLIPDKGFEWIGWIKPLWGAVSYARQLQGRVSMTRQLSQDPDDPDWGVAYMEFSGLTPADTAEYFCVRRGSCDYCGDFPWQYWCQGTVVVVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPK |
Light Chain: F
Mutation: NULL
| >6V8Z_F|Chain F, L, R|VRC03 Fab Light Chain|Homo sapiens (9606) EIVLTQSPGILSLSPGETATLFCKASQGGNAMTWYQKRRGQVPRLLIYDTSRRASGVPDRFVGSGSGTDFFLTINKLDREDFAVYYCQQFEFFGLGSELEVHRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGE |
Antigen
Chain: A
Mutation: NULL
| >6V8Z_A|Chain A, G, M|Envelope glycoprotein gp120|Human immunodeficiency virus 1 (11676) ENLWVTVYYGVPVWKDAETTLFCASDAKAYETEKHNIWATHACVPTDPNPQEIHLENVTEEFNMWKNNMVEQMHTDIISLWDQSLKPCVKLTPLCVTLQCTNVTNAITDDMRGELKNCSFNMTTELRDKKQKVYSLFYRLDVVQINENQGNRSNNSNKEYRLINCNTSAITMVCPKLSFEPIPIHYCAPAGFAILKCKDKKFNGTGPCPSVSTVQCTHGIKPVLSTQLLLNGSLAEEEVMIRSENITNNAKNILVQFNTPVQINCTRPLNLTRKSIRIGPGQAFYAMGDIIGDIRQAHCNVSKATWNETLGKVVKQLRKHFGNNTIIRFANSSGGDLEVTTHSFNCGGEFFYCNTSGLFNSTWISNTSVQGSNSTGSNDSITLPCRIKMIINMWQRIGQAMYAPPIQGVIRCVSNITGLILTRDGGSTNSTTETFRPGGGDMRDNWRSELYKYKVVKIEPLGVAPTRCKRRV |
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 C: ARG30 HIS35 GLU46 TRP47 TRP50 LEU53 TRP54 GLY55 ALA56 VAL57 SER58 TYR59 ALA60 ARG61 GLN62 GLN64 ARG71 LEU73 SER74 GLN75 ASP99 F: GLU1 ILE2 GLN27 ASN31 PHE91 GLU96 PHE97 A: LYS97 THR198 ASN276 THR278 ASN279 ASN280 ALA281 LYS282 ASN283 SER365 GLY366 GLY367 ASP368 GLU370 VAL371 ASN425 MET426 TRP427 GLN428 ILE430 GLY431 THR455 ARG456 ASP457 GLY458 GLY459 SER460 THR461 ASN462 SER463 THR465 GLU466 THR467 ARG469 GLY472 GLY473 ASP474 |
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)
