Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 4000 |
| PDBID: | 7KRA |
| Chains: | IJ_A |
| Organism: | Saccharomyces cerevisiae, Homo sapiens |
| Method: | EM |
| Resolution (Å): | 3.20 |
| Reference: | 10.7554/eLife.62611 |
| Antibody | |
| Antibody: | DH4 Fab |
| Antibody mutation: | No |
| INN (Clinical Trial): | |
| Antigen | |
| Antigen: | ER membrane protein complex subunit 1 |
| Antigen mutation: | No |
| Durg Target: | |
Sequence information
Antibody
Heavy Chain: I
Mutation: NULL
| >7KRA_I|Chain I|Fab DH4 heavy chain|Homo sapiens (9606) MAQVQLQQWGAGLLKPSETLSLTCAVYGGSFSGYYWSWIRQPPGKGLEWIGEINHSGSTNYNPSLKSRVTISVDTSKNQFSLKLSSVTAADTAVYYCARGLAGRGYYGSGSYLRWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCAAAHHHHHHGAAEQKLISEEDLNGAA |
Light Chain: J
Mutation: NULL
| >7KRA_J|Chain J|Fab DH4 light chain|Homo sapiens (9606) LFAIPLVVPFYSHSALDVVMTQSPLSLPVTPGEPASISCRSSQTLMNRNGNNFLDWYLQKPGQSPQLLIYLGSNRAPGVPDRFSGSGSGTDFTLRISRVEPEDVGVYYCMQALQTPSFGGGTKVEIRRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC |
Antigen
Chain: A
Mutation: NULL
| >7KRA_A|Chain A|ER membrane protein complex subunit 1|Saccharomyces cerevisiae (4932) MKITCTDLVYVFILLFLNTSCVQAVFSDDAFITDWQLANLGPWEKVIPDSRDRNRVLILSNPTETSCLVSSFNVSSGQILFRNVLPFTIDEIQLDSNDHNAMVCVNSSSNHWQKYDLHDWFLLEEGVDNAPSTTILPQSSYLNDQVSIKNNELHILDEQSKLAEWKLELPQGFNKVEYFHREDPLALVLNVNDTQYMGFSANGTELIPVWQRDEWLTNVVDYAVLDVFDSRDVELNKDMKAELDSNSLWNAYWLRLTTNWNRLINLLKENQFSPGRVFTKLLALDAKDTTVSDLKFGFAKILIVLTHDGFIGGLDMVNKGQLIWKLDLEIDQGVKMFWTDKNHDELVVFSHDGHYLTIEVTKDQPIIKSRSPLSERKTVDSVIRLNEHDHQYLIKFEDKDHLLFKLNPGKNTDVPIVANNHSSSHIFVTEHDTNGIYGYIIENDTVKQTWKKAVNSKEKMVAYSKRETTNLNTLGITLGDKSVLYKYLYPNLAAYLIANEEHHTITFNLIDTITGEILITQEHKDSPDFRFPMDIVFGEYWVVYSYFSSEPVPEQKLVVVELYESLTPDERLSNSSDNFSYDPLTGHINKPQFQTKQFIFPEIIKTMSISKTTDDITTKAIVMELENGQITYIPKLLLNARGKPAEEMAKDKKKEFMATPYTPVIPINDNFIITHFRNLLPGSDSQLISIPTNLESTSIICDLGLDVFCTRITPSGQFDLMSPTFEKGKLLITIFVLLVITYFIRPSVSNKKLKSQWLIK |
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)
| Chain residues position delta_SASA
: residuesposition I: ALA2 GLN3 VAL4 GLN5 GLN7 TYR27 GLY28 GLY29 SER30 PHE31 SER32 GLY33 TYR34 TYR35 ASN54 HIS55 SER56 LYS77 ASN78 GLN79 PHE80 ARG99 LEU101 ALA102 GLY103 ARG104 GLY105 TYR106 SER109 ARG114 J: ASN47 ARG48 ASN49 GLY50 ASN51 ASN52 PHE53 TYR70 LEU71 SER73 ASN74 ARG75 PRO77 GLY78 A: PRO42 TRP43 GLU44 LYS45 PRO62 THR63 GLU64 THR88 ILE89 ASP90 ILE135 LEU136 GLN138 SER139 SER140 TYR141 LEU142 ASN143 ASP144 VAL146 SER147 ILE148 LYS149 ASN150 ASN151 LEU156 GLU158 LYS161 LEU169 GLN171 GLY172 PHE173 ASN174 LYS175 ASN190 ASP193 THR194 TYR196 ASP308 GLY309 PHE310 ASP327 LEU328 GLU329 ASP331 GLN332 HIS351 ASP352 |
2、We defined interacting paratope-epitope residues by a distance cutoff of < 6 Å . Two amino acids are considered as interacting residues if they have at least one atom within a distance of 6 Å from any atom.
Interacting residues (Atom distance based)
