Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 6257 |
| PDBID: | 8GJE |
| Chains: | IK_D |
| Organism: | Human immunodeficiency virus 1, Homo sapiens |
| Method: | EM |
| Resolution (Å): | 3.40 |
| Reference: | 10.1371/journal.ppat.1011601 |
| Antibody | |
| Antibody: | 3BNC117 Fab |
| Antibody mutation: | No |
| INN (Clinical Trial): | |
| Antigen | |
| Antigen: | HIV-1 CZA97.012 SOSIP.664 envelope glycoprotein - gp120 |
| Antigen mutation: | Yes |
| Durg Target: | P00750 |
Sequence information
Antibody
Heavy Chain: I
Mutation: NULL
| >8GJE_I|Chain C[auth G], G[auth H], K[auth I]|3BNC117 Fab heavy chain|Homo sapiens (9606) QVQLLQSGAAVTKPGASVRVSCEASGYNIRDYFIHWWRQAPGQGLQWVGWINPKTGQPNNPRQFQGRVSLTRHASWDFDTYSFYMDLKALRSDDTAVYFCARQRSDYWDFDVWGSGTQVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSC |
Light Chain: K
Mutation: NULL
| >8GJE_K|Chain D[auth J], H[auth K], L|3BNC117 kappa light chain|Homo sapiens (9606) DIQMTQSPSSLSASVGDTVTITCQANGYLNWYQQRRGKAPKLLIYDGSKLERGVPSRFSGRRWGQEYNLTINNLQPEDIATYFCQVYEFVVPGTRLDLKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC |
Antigen
Chain: D
Mutation: A491C/E499R/K500R
| >8GJE_D|Chain A, E[auth C], I[auth D]|CZA97.12 SOSIP.664 Envelope glycoprotein gp120|Human immunodeficiency virus 1 (11676) MDAMKRGLCCVLLLCGAVFVSPSQEIHARFRRGARVGNMWVTVYYGVPVWTDAKTTLFCASDTKAYDREVHNVWATHACVPTDPNPQEIVLENVTENFNMWKNDMVDQMHEDIISLWDQSLKPCVKLTPLCVTLHCTNATFKNNVTNDMNKEIRNCSFNTTTEIRDKKQQGYALFYRPDIVLLKENRNNSNNSEYILINCNASTITQACPKVNFDPIPIHYCAPAGYAILKCNNKTFSGKGPCNNVSTVQCTHGIKPVVSTQLLLNGSLAEKEIIIRSENLTDNVKTIIVHLNKSVEIVCTRPNNNTRKSMRIGPGQTFYATGDIIGDIRQAYCNISGSKWNETLKRVKEKLQENYNNNKTIKFAPSSGGDLEITTHSFNCRGEFFYCNTTRLFNNNATEDETITLPCRIKQIINMWQGVGRAMYAPPIAGNITCKSNITGLLLVRDGGEDNKTEEIFRPGGGNMKDNWRSELYKYKVIELKPLGIAPTGCKRRVVERRRRRR |
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: ARG30 PHE33 TRP47 TRP50 LYS53 THR54 GLY55 GLN56 PRO57 ASN58 ASN59 PRO60 ARG61 GLN62 GLN64 TRP71 PHE73 GLN95 ASP98 K: ASP1 ILE2 GLN3 TYR32 TYR91 GLU96 PHE97 D: LYS97 ALA198 GLU275 ASN276 THR278 ASP279 ASN280 VAL281 LYS282 ASN354 LYS357 SER364 SER365 GLY366 GLY367 ASP368 ILE371 GLN428 GLY429 VAL430 VAL455 ARG456 ASP457 GLY458 GLY459 GLU460 ASP461 ASN462 LYS463 GLU465 ILE467 ARG469 PRO470 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)
