Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 1253 |
| PDBID: | 5D9Q |
| Chains: | O_J |
| Organism: | Human immunodeficiency virus 1, Homo sapiens |
| Method: | XRD |
| Resolution (Å): | 4.40 |
| Reference: | 10.1371/journal.ppat.1005815 |
| Antibody | |
| Antibody: | NIH45-46 scFv |
| Antibody mutation: | No |
| INN (Clinical Trial): | |
| Antigen | |
| Antigen: | HIV-1 BG505 SOSIP gp120 |
| Antigen mutation: | No |
| Durg Target: | |
Sequence information
Antibody
Chain: O
Mutation: NULL
| >5D9Q_O|Chain E[auth D], J[auth I], O|NIH45-46 single chain Fv|Homo sapiens (9606) QVRLSQSGGQMKKPGESMRLSCRASGYEFLNCPINWIRLAPGRRPEWMGWLKPRGGAVNYARKFQGRVTMTRDVYSDTAFLELRSLTSDDTAVYFCTRGKYCTARDYYNWDFEHWGRGAPVTVSSGGGGSGGGGSGGGGSEIVLTQSPATLSLSPGETAIISCRTSQSGSLAWYQQRPGQAPRLVIYSGSTRAAGIPDRFSGSRWGADYNLSISNLESGDFGVYYCQQYEFFGQGTKVQVD |
Antigen
Chain: J
Mutation: NULL
| >5D9Q_J|Chain A, F[auth G], K[auth J]|Envelope glycoprotein gp120|Human immunodeficiency virus 1 (11676) AENLWVTVYYGVPVWKDAETTLFCASDAKAYETEKHNVWATHACVPTDPNPQEIHLENVTEEFNMWKNNMVEQMHTDIISLWDQSLKPCVKLTPLCVTLQCTNVTNNITDDMRGELKNCSFNMTTELRDKKQKVYSLFYRLDVVQINENQGNRSNNSNKEYRLINCNTSAITQACPKVSFEPIPIHYCAPAGFAILKCKDKKFNGTGPCPSVSTVQCTHGIKPVVSTQLLLNGSLAEEEVMIRSENITNNAKNILVQFNTPVQINCTRPNNNTRKSIRIGPGQAFYATGDIIGDIRQAHCNVSKATWNETLGKVVKQLRKHFGNNTIIRFANSSGGDLEVTTHSFNCGGEFFYCNTSGLFNSTWISNTSVQGSNSTGSNDSITLPCRIKQIINMWQRIGQAMYAPPIQGVIRCVSNITGLILTRDGGANNTSTETFRPGGGDMRDNWRSELYKYKVVKIEPLGVAPTRCKRR |
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 PRO33 ARG44 TRP47 TRP50 ARG53 GLY54 GLY55 ALA56 VAL57 ASN58 TYR59 ALA60 ARG61 GLN64 MET69 THR70 ARG71 VAL73 TYR74 TYR99 TYR100 ASN101 TRP102 VAL203 GLN227 SER228 TYR289 GLU290 PHE291 J: GLU49 TRP96 LYS97 ASN98 ASN99 GLU102 HIS105 THR198 GLU275 ASN276 THR278 ASN279 ASN280 ALA281 LYS282 ASN283 SER365 GLY366 GLY367 ASP368 VAL371 ASN425 TRP427 GLN428 ILE430 THR455 ARG456 ASP457 GLY458 GLY459 ALA460 ASN461 THR463 THR465 GLU466 THR467 ARG469 GLY471 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)
