Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 1106 |
| PDBID: | 4YDI |
| Chains: | HL_G |
| Organism: | Human immunodeficiency virus 1, Homo sapiens |
| Method: | XRD |
| Resolution (Å): | 3.45 |
| Reference: | 10.1016/j.cell.2015.05.007 |
| Antibody | |
| Antibody: | Z258-VRC27.01 Fab |
| Antibody mutation: | No |
| INN (Clinical Trial): | |
| Antigen | |
| Antigen: | HIV-1 clade A strain Q23.17 gp120 |
| Antigen mutation: | No |
| Durg Target: | |
Sequence information
Antibody
Heavy Chain: H
Mutation: NULL
| >4YDI_H|Chain B[auth H]|HEAVY CHAIN OF ANTIBODY Z258-VRC27.01|Homo sapiens (9606) SQRLVQSGPQVRKPGSSVRISCETSGYTFNAYILHWFRQAPGRSFEWMGWIKPKFGAVNYAHSFQGRITLTRDIYRETAFLDLTGLRFDDTAVYYCARDRLYDGSSWRLDPWGQGTRVVVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDK |
Light Chain: L
Mutation: NULL
| >4YDI_L|Chain C[auth L]|LIGHT CHAIN OF ANTIBODY Z258-VRC27.01|Homo sapiens (9606) DIQMTQSPSSLAVSVGGRVTITCRASQGIGSDLHWYQQKRGRPPKILIHHASAREEGVPSRFGGSGSHTPFIFTINDLQLDDVATYYCQVIESFGQGTRLDINRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC |
Antigen
Chain: G
Mutation: NULL
| >4YDI_G|Chain A[auth G]|Envelope glycoprotein gp160|Human immunodeficiency virus 1 (11676) VWRDADTTLFCASDAKAYETEKHNVWATHACVPTDPNPQEIHLDNVTEKFNMWKNNMVEQMHTDIISLWDQSLKPCVKLTGGSAITQACPKVSFEPIPIHYCTPAGFAILKCKDEGFNGTGLCKNVSTVQCTHGIKPVVSTQLLLNGSLAEKNITIRSENITNNAKIIIVQLVQPVTIKCIRPNNGGSGSGGDIRQAHCNVTRSRWNKTLQEVAEKLRTYFGNKTIIFANSSGGDLEITTHSFNCGGEFFYCNTSGLFNSTWYVNSTWNDTDSTQESNDTITLPCRIKQIINMWQRAGQAMYAPPIPGVIKCESNITGLLLTRDGGKDNNVNETFRPGGGDMRDNWRSELYKYKVVEIE |
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)
| H: ASN30 ILE33 GLU46 TRP47 TRP50 LYS53 PHE54 GLY55 ALA56 VAL57 ASN58 TYR59 ALA60 HIS61 GLN64 ARG71 ILE73 TYR74 ASP99 L: ILE2 GLN3 ASP32 ILE91 GLU96 G: LYS97 LEU122 GLY124 ASN276 THR278 ASN279 ASN280 ALA281 LYS282 ILE283 SER365 GLY366 GLY367 ASP368 GLU370 ILE371 ASN425 MET426 TRP427 ARG429 ALA430 GLY431 GLN432 THR455 ARG456 ASP457 GLY458 GLY459 LYS460 ASP461 ASN462 ARG469 GLY472 GLY473 ASP474 MET475 ARG476 ARG480 |
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)
