Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 1920 |
| PDBID: | 5WDU |
| Chains: | O_F |
| Organism: | Human immunodeficiency virus 1, Homo sapiens |
| Method: | XRD |
| Resolution (Å): | 7.00 |
| Reference: | 10.1016/j.celrep.2017.07.077 |
| Antibody | |
| Antibody: | NIH45-46 scFv |
| Antibody mutation: | No |
| INN (Clinical Trial): | |
| Antigen | |
| Antigen: | HIV-1 BG505 SOSIP.664 H72C-H564C gp160 |
| Antigen mutation: | No |
| Durg Target: | |
Sequence information
Antibody
Chain: O
Mutation: NULL
| >5WDU_O|Chain B[auth D], D[auth O], F[auth W]|bnAb NIH45-46 scFv|Homo sapiens (9606) QVRLSQSGGQMKKPGESMRLSCRASGYEFLNCPINWIRLAPGRRPEWMGWLKPRGGAVNYARKFQGRVTMTRDVYSDTAFLELRSLTSDDTAVYFCTRGKYCTARDYYNWDFEHWGRGAPVTVSSGGGGSGGGGSGGGGSEIVLTQSPATLSLSPGETAIISCRTSQSGSLAWYQQRPGQAPRLVIYSGSTRAAGIPDRFSGSRWGADYNLSISNLESGDFGVYYCQQYEFFGQGTKVQVDGTKHHHHHH |
Antigen
Chain: F
Mutation: NULL
| >5WDU_F|Chain A[auth F], C[auth G], E[auth Q]|Envelope glycoprotein gp160|Human immunodeficiency virus 1 (11676) ENLWVTVYYGVPVWKDAETTLFCASDAKAYETEKHNVWATCACVPTDPNPQEIHLENVTEEFNMWKNNMVEQMHTDIISLWDQSLKPCVKLTPLCVTLQCTNVTNNITDDMRGELKNCSFNMTTELRDKKQKVYSLFYRLDVVQINENQGNRSNNSNKEYRLINCNTSAITQACPKVSFEPIPIHYCAPAGFAILKCKDKKFNGTGPCPSVSTVQCTHGIKPVVSTQLLLNGSLAEEEVMIRSENITNNAKNILVQFNTPVQINCTRPNNNTRKSIRIGPGQAFYATGDIIGDIRQAHCNVSKATWNETLGKVVKQLRKHFGNNTIIRFANSSGGDLEVTTHSFNCGGEFFYCNTSGLFNSTWISNTSVQGSNSTGSNDSITLPCRIKQIINMWQRIGQAMYAPPIQGVIRCVSNITGLILTRDGGANNTSTETFRPGGGDMRDNWRSELYKYKVVKIEPLGVAPTRCKRR |
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)
| O: LEU30 ASN31 PRO33 ARG44 TRP47 TRP50 LYS52 ARG54 GLY55 GLY56 ALA57 VAL58 ASN59 TYR60 ALA61 ARG62 GLN65 MET70 THR71 ARG72 VAL74 TYR75 TYR101 ALA104 ARG105 ASP106 TYR107 TYR108 ASN109 TRP110 VAL125 GLN149 SER150 TYR211 GLU212 PHE213 F: GLU49 TRP96 LYS97 ASN98 ASN99 GLU102 HIS105 ASN197 THR198 GLU275 ASN276 THR278 ASN279 ASN280 ALA281 LYS282 ASN283 ARG360 SER364 SER365 GLY366 GLY367 ASP368 VAL371 TRP427 GLN428 ILE430 THR455 ARG456 ASP457 GLY458 GLY459 ALA460 ASN461 THR463 THR465 GLU466 THR467 ARG469 GLY471 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)
