Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 1836 |
| PDBID: | 5VN8 |
| Chains: | FJ_D |
| Organism: | Human immunodeficiency virus 1, Homo sapiens |
| Method: | EM |
| Resolution (Å): | 3.60 |
| Reference: | 10.1038/nature23010 |
| Antibody | |
| Antibody: | b12 Fab |
| Antibody mutation: | No |
| INN (Clinical Trial): | |
| Antigen | |
| Antigen: | HIV-1 B41 SOSIP.664 gp160 |
| Antigen mutation: | Yes |
| Durg Target: | P00750 |
Sequence information
Antibody
Heavy Chain: F
Mutation: NULL
| >5VN8_F|Chain C[auth F], G[auth H], K[auth I]|b12 Fab heavy chain|Homo sapiens (9606) QVQLVQSGAEVKKPGASVKVSCQASGYRFSNFVIHWVRQAPGQRFEWMGWINPYNGNKEFSAKFQDRVTFTADTSANTAYMELRSLRSADTAVYYCARVGPYSWDDSPQDNYYMDVWGKGTTVIVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKAEPKSC |
Light Chain: J
Mutation: NULL
| >5VN8_J|Chain D[auth J], H[auth K], L|b12 Fab light chain|Homo sapiens (9606) EIVLTQSPGTLSLSPGERATFSCRSSHSIRSRRVAWYQHKPGQAPRLVIHGVSNRASGISDRFSGSGSGTDFTLTITRVEPEDFALYYCQVYGASSYTFGQGTKLERKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLRSPVTKSFNRGEC |
Antigen
Chain: D
Mutation: A512C
| >5VN8_D|Chain A[auth D], E, I[auth G]|Envelope glycoprotein gp160|Human immunodeficiency virus 1 (11676) MDAMKRGLCCVLLLCGAVFVSPSQEIHARFRRGARAAKKWVTVYYGVPVWKEATTTLFCASDAKAYDTEVHNVWATHACVPTDPNPQEIVLGNVTENFNMWKNNMVEQMHEDIISLWDQSLKPCVKLTPLCVTLNCNNVNTNNTNNSTNATISDWEKMETGEMKNCSFNVTTSIRDKIKKEYALFYKLDVVPLENKNNINNTNITNYRLINCNTSVITQACPKVSFEPIPIHYCAPAGFAILKCNSKTFNGSGPCTNVSTVQCTHGIRPVVSTQLLLNGSLAEEEIVIRSENITDNAKTIIVQLNEAVEINCTRPNNNTRKSIHIGPGRAFYATGDIIGNIRQAHCNISKARWNETLGQIVAKLEEQFPNKTIIFNHSSGGDPEIVTHSFNCGGEFFYCNTTPLFNSTWNNTRTDDYPTGGEQNITLQCRIKQIINMWQGVGKAMYAPPIRGQIRCSSNITGLLLTRDGGRDQNGTETFRPGGGNMRDNWRSELYKYKVVKIEPLGIAPTACKRRV |
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)
| F: GLN1 GLY26 ARG28 SER30 ASN31 PHE32 VAL33 TYR53 ASN54 GLY55 ASN56 LYS57 GLU58 THR73 ASN76 VAL95 GLY96 PRO97 TYR98 J: GLU1 SER26 SER27 ARG29 SER30 ARG31 TYR91 ALA93 SER94 D: LYS178 LEU179 VAL181 VAL182 PRO183 LEU184 ASN187 THR189 ARG192 ILE194 ASN195 ASN197 THR198 THR257 ALA281 HIS363 SER365 GLY366 GLY367 ASP368 PRO369 GLU370 ILE371 VAL372 THR373 TYR384 ASN386 GLN417 ARG419 ASN425 GLN428 GLY429 VAL430 GLY431 THR455 ARG456 ASP457 GLY458 ARG460 ASP461 ARG469 GLY471 GLY472 GLY473 ASN474 |
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)
