Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 2048 |
| PDBID: | 6B0N |
| Chains: | DE_G |
| Organism: | Homo sapiens, Human immunodeficiency virus 1 |
| Method: | XRD |
| Resolution (Å): | 3.40 |
| Reference: | 10.1038/s41467-018-04272-y |
| Antibody | |
| Antibody: | PGV19 Fab |
| Antibody mutation: | No |
| INN (Clinical Trial): | |
| Antigen | |
| Antigen: | Envelope glycoprotein gp140 |
| Antigen mutation: | No |
| Durg Target: | |
Sequence information
Antibody
Heavy Chain: D
Mutation: NULL
| >6B0N_D|Chain A[auth D]|PGV19 Fab heavy chain|Homo sapiens (9606) EVRLVQSGAEVKKPGASVRVSCAASGYTFTDFDIHWLRQAPGRGLEWMGWVRPLGGGVSYARQFQGRVTMTRDFYIDTAFMDFRNLKMDDTALYFCARMGAAREWDFQYWGQGTRVLVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSC |
Light Chain: E
Mutation: NULL
| >6B0N_E|Chain B[auth E]|PGV19 light chain|Homo sapiens (9606) QSALTQPASVSGSPGQSITISCTASSDFRGFSSVSWYQQVPGRAPKLLIFSVNRRPSGISHRFSGSKSGNTASLTISGLQIEDEADYHCNAYEFFGGGTKVFVLGQPKAAPSVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSYLSLTPEQWKSHKSYSCQVTHEGSTVEKTVAPTEC |
Antigen
Chain: G
Mutation: NULL
| >6B0N_G|Chain C[auth G]|Envelope glycoprotein gp140|Human immunodeficiency virus 1 (11676) AENLWVTVYYGVPVWKDAETTLFCASDAKAYETEKHNVWATHACVPTDPNPQEIHLENVTEEFNMWKNNMVEQMHTDIISLWDQSLKPCVKLTPLCVTLQCTNVTNNITDDMRGELKNCSFNMTTELRDKKQKVYSLFYRLDVVQINENQGNRSNNSNKEYRLINCNTSAITQACPKVSFEPIPIHYCAPAGFAILKCKDKKFNGTGPCPSVSTVQCTHGIKPVVSTQLLLNGSLAEEEVMIRSENITNNAKNILVQFNTPVQINCTRPNNNTRKSIRIGPGQAFYATGDIIGDIRQAHCNVSKATWNETLGKVVKQLRKHFGNNTIIRFANSSGGDLEVTTHSFNCGGEFFYCNTSGLFNSTWISNTSVQGSNSTGSNDSITLPCRIKQIINMWQRIGQAMYAPPIQGVIRCVSNITGLILTRDGGSTNSTTETFRPGGGDMRDNWRSELYKYKVVKIEPLGVAPTRAKRRVVGGGGGSGGGGSAVGIGAVFLGFLGAAGSTMGAASMTLTVQARNLLSGIVQQQSNLLRAPEAQQHLLKLTVWGIKQLQARVLAVERYLRDQQLLGIWGCSGKLICTTNVPWNSSWSNRNLSEIWDNMTWLQWDKEISNYTQIIYGLLEESQNQQEKNEQDLLALD |
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)
| D: ASP33 HIS35 TRP47 TRP50 LEU53 GLY54 GLY55 GLY56 VAL57 SER58 TYR59 ALA60 ARG61 GLN62 GLN64 THR68 THR70 ARG71 PHE73 TYR74 MET95 ARG99 E: SER2 ALA3 PHE27 ARG28 GLY29 SER31 TYR91 GLU96 PHE97 G: THR198 ASN276 THR278 ASN279 ASN280 ALA281 LYS282 ASN283 HIS352 PHE353 GLY354 ARG360 SER365 GLY366 GLY367 ASP368 VAL371 ASN425 TRP427 GLN428 ILE430 THR455 ARG456 ASP457 GLY458 GLY459 SER460 THR461 ASN462 SER463 THR465 GLU466 THR467 ARG469 GLY473 ASP474 |
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)
