Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 6634 |
| PDBID: | 3J5M |
| Chains: | LK_I |
| Organism: | Human immunodeficiency virus 1, Homo sapiens |
| Method: | EM |
| Resolution (Å): | 5.80 |
| Reference: | 10.1126/science.1245627 |
| Antibody | |
| Antibody: | PGV04 Fab |
| Antibody mutation: | No |
| INN (Clinical Trial): | |
| Antigen | |
| Antigen: | HIV-1 BG505 SOSIP gp120 |
| Antigen mutation: | Yes |
| Durg Target: | |
Sequence information
Antibody
Heavy Chain: L
Mutation: NULL
| >3J5M_L|Chain D, H, L|PGV04 heavy chain|Homo sapiens (9606) QVQLVQSGSGVKKPGASVRVSCWTSEDIFERTELIHWVRQAPGQGLEWIGWVKTVTGAVNFGSPDFRQRVSLTRDRDLFTAHMDIRGLTQGDTATYFCARQKFYTGGQGWYFDLWGRGTLIVVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSC |
Light Chain: K
Mutation: NULL
| >3J5M_K|Chain C, G, K|PGV04 light chain|Homo sapiens (9606) EIVLTQSPGTLSLSPGETASLSCTAASYGHMTWYQKKPGQPPKLLIFATSKRASGIPDRFSGSQFGKQYTLTITRMEPEDFARYYCQQLEFFGQGTRLEIRRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC |
Antigen
Chain: I
Mutation: T301N/A469C
| >3J5M_I|Chain A, E, I|BG505 SOSIP gp120|Human immunodeficiency virus 1 (11676) AENLWVTVYYGVPVWKDAETTLFCASDAKAYETEKHNVWATHACVPTDPNPQEIHLENVTEEFNMWKNNMVEQMHTDIISLWDQSLKPCVKLTPLCVTLQCTNVTNNITDDMRGELKNCSFNMTTELRDKKQKVYSLFYRLDVVQINENQGNRSNNSNKEYRLINCNTSAITQACPKVSFEPIPIHYCAPAGFAILKCKDKKFNGTGPCPSVSTVQCTHGIKPVVSTQLLLNGSLAEEEVMIRSENITNNAKNILVQFNTPVQINCTRPNNNTRKSIRIGPGQAFYATGDIIGDIRQAHCNVSKATWNETLGKVVKQLRKHFGNNTIIRFANSSGGDLEVTTHSFNCGGEFFYCNTSGLFNSTWISNTSVQGSNSTGSNDSITLPCRIKQIINMWQRIGQAMYAPPIQGVIRCVSNITGLILTRDGGSTNSTTETFRPGGGDMRDNWRSELYKYKVVKIEPLGVAPTRCKRRVVG |
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)
| K: GLU1 ILE2 VAL3 SER27 TYR30 GLY31 GLN90 LEU91 GLU96 PHE97 L: GLU30 GLU33 LEU34 TRP50 VAL52 THR53 GLY54 ALA55 VAL56 ASN57 PHE58 GLY59 SER60 PRO61 ARG64 ARG71 ASP72 ARG73 ASP74 GLN95 PHE97 TYR98 THR99 I: LYS97 THR198 GLU275 ASN276 THR278 ASN279 ASN280 ALA281 LYS282 ASN283 ARG360 ALA362 SER365 GLY366 GLY367 ASP368 VAL371 TRP427 GLN428 ARG429 ILE430 THR455 ARG456 ASP457 GLY458 GLY459 SER460 THR461 THR467 ARG469 GLY472 GLY473 ASP474 ARG476 |
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)
