Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 2832 |
| PDBID: | 6SNI |
| Chains: | HL_X |
| Organism: | Saccharomyces cerevisiae, synthetic construct |
| Method: | EM |
| Resolution (Å): | 3.00 |
| Reference: | 10.1038/s41586-020-2044-z |
| Antibody | |
| Antibody: | 6AG9 Fab |
| Antibody mutation: | No |
| INN (Clinical Trial): | |
| Antigen | |
| Antigen: | Dolichyl pyrophosphate Man9GlcNAc2 alpha-1,3-glucosyltransferase |
| Antigen mutation: | No |
| Durg Target: | |
Sequence information
Antibody
Heavy Chain: H
Mutation: NULL
| >6SNI_H|Chain B[auth H]|6AG9-Fab heavy chain|synthetic construct (32630) EISEVQLVESGGGLVQPGGSLRLSCAASGFNVYSSSIHWVRQAPGKGLEWVASISSYSGYTSYADSVKGRFTISADTSKNTAYLQMNSLRAEDTAVYYCAREYWSWYSYSYGIDYWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTHT |
Light Chain: L
Mutation: NULL
| >6SNI_L|Chain C[auth L]|6AG9-Fab light chain|synthetic construct (32630) SDIQMTQSPSSLSASVGDRVTITCRASQSVSSAVAWYQQKPGKAPKLLIYSASSLYSGVPSRFSGSRSGTDFTLTISSLQPEDFATYYCQQSYWVGYPITFGQGTKVEIKRTVAAPSVFIFPPSDSQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC |
Antigen
Chain: X
Mutation: NULL
| >6SNI_X|Chain A[auth X]|Dolichyl pyrophosphate Man9GlcNAc2 alpha-1,3-glucosyltransferase|Saccharomyces cerevisiae (4932) GPGGSTGRLAGAGGEFVDMAIGKRLLVNKPAEESFYASPMYDFLYPFRPVGNQWLPEYIIFVCAVILRCTIGLGPYSGKGSPPLYGDFEAQRHWMEITQHLPLSKWYWYDLQYWGLDYPPLTAFHSYLLGLIGSFFNPSWFALEKSRGFESPDNGLKTYMRSTVIISDILFYFPAVIYFTKWLGRYRNQSPIGQSIAASAILFQPSLMLIDHGHFQYNSVMLGLTAYAINNLLDEYYAMAAVCFVLSICFKQMALYYAPIFFAYLLSRSLLFPKFNIARLTVIAFATLATFAIIFAPLYFLGGGLKNIHQCIHRIFPFARGIFEDKVANFWCVTNVFVKYKERFTIQQLQLYSLIATVIGFLPAMIMTLLHPKKHLLPYVLIACSMSFFLFSFQVHEKTILIPLLPITLLYSSTDWNVLSLVSWINNVALFTLWPLLKKDGLHLQYAVSFLLSNWLIGNFSFITPRFLPKSLTPGPSISSINSDYRRRSLLPYNVVWKSFIIGTYIAMGFYHFLDQFVAPPSKYPDLWVLLNCAVGFICFSIFWLWSYYKIFTSGSKSMKDL |
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: ASN28 TYR30 SER31 SER52 TYR53 SER54 GLY55 TYR56 THR73 SER74 ASN76 TYR99 TRP100 SER101 TRP102 TYR103 SER104 TYR105 L: GLN27 SER28 VAL29 SER30 SER31 ALA32 ARG66 TYR92 TRP93 VAL94 GLY95 X: TRP90 LEU93 GLN94 LYS288 HIS291 GLN292 ILE294 HIS295 ARG296 PHE298 PRO299 PHE300 ALA301 ARG302 GLY303 ILE304 GLU306 LYS323 GLU324 ARG325 PHE326 THR327 ILE328 GLN329 GLN330 GLN332 LEU333 LEU336 |
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)
