Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 4329 |
| PDBID: | 7MN8 |
| Chains: | DC_B |
| Organism: | Homo sapiens, Escherichia coli K-12 |
| Method: | EM |
| Resolution (Å): | 3.45 |
| Reference: | 10.1038/s41586-021-04084-z |
| Antibody | |
| Antibody: | Trastuzumab Fab |
| Antibody mutation: | No |
| INN (Clinical Trial): | Anbenitamab(Phase-II/III); Anvatabart(Phase-II/III); Cinrebafusp(Phase-II); Coprelotamab(Phase-III); Fidasimtamab(Phase-I); Runimotamab(Phase-I); Timigutuzumab(Phase-I); Trastuzumab(Approved); Zanidatamab(Preregistration); |
| Antigen | |
| Antigen: | Receptor tyrosine-protein kinase erbB-2 |
| Antigen mutation: | No |
| Durg Target: | P04626; P0AEX9; |
Sequence information
Antibody
Heavy Chain: D
Mutation: NULL
| >7MN8_D|Chain E[auth D]|Trastuzumab Fab Heavy Chain|Homo sapiens (9606) EVQLVESGGGLVQPGGSLRLSCAASGFNIKDTYIHWVRQAPGKGLEWVARIYPTNGYTRYADSVKGRFTISADTSKNTAYLQMNSLRAEDTAVYYCSRWGGDGFYAMDYWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTHTGGSHHHHHH |
Light Chain: C
Mutation: NULL
| >7MN8_C|Chain D[auth C]|Trastuzumab Fab Light Chain|Homo sapiens (9606) DIQMTQSPSSLSASVGDRVTITCRASQDVNTAVAWYQQKPGKAPKLLIYSASFLYSGVPSRFSGSRSGTDFTLTISSLQPEDFATYYCQQHYTTPPTFGQGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGECGGSDYKDDDDK |
Antigen
Chain: B
Mutation: NULL
| >7MN8_B|Chain C[auth B]|Receptor tyrosine-protein kinase erbB-2,Maltose/maltodextrin-binding periplasmic protein|Homo sapiens (9606) MELAALCRWGLLLALLPPGAASTQVCTGTDMKLRLPASPETHLDMLRHLYQGCQVVQGNLELTYLPTNASLSFLQDIQEVQGYVLIAHNQVRQVPLQRLRIVRGTQLFEDNYALAVLDNGDPLNNTTPVTGASPGGLRELQLRSLTEILKGGVLIQRNPQLCYQDTILWKDIFHKNNQLALTLIDTNRSRACHPCSPMCKGSRCWGESSEDCQSLTRTVCAGGCARCKGPLPTDCCHEQCAAGCTGPKHSDCLACLHFNHSGICELHCPALVTYNTDTFESMPNPEGRYTFGASCVTACPYNYLSTDVGFCTLVCPLHNQEVTAEDGTQRCEKCSKPCARVCYGLGMEHLREVRAVTSANIQEFAGCKKIFGSLAFLPESFDGDPASNTAPLQPEQLQVFETLEEITGYLYISAWPDSLPDLSVFQNLQVIRGRILHNGAYSLTLQGLGISWLGLRSLRELGSGLALIHHNTHLCFVHTVPWDQLFRNPHQALLHTANRPEDECVGEGLACHQLCARGHCWGPGPTQCVNCSQFLRGQECVEECRVLQGLPREYVNARHCLPCHPECQPQNGSVTCFGPEADQCVACAHYKDPPFCVARCPSGVKPDLSYMPIWKFPDEEGACQPCPINCTHSCVDLDDKGCPAEQRASPLTSIISAVVGILLVVVLGVVFGILIKRRQQKIRKYTMRRLLQETELVEPLTPSGAMPNQAQMRILKETELRKVKVLGSGAFGTVYKGIWIPDGENVKIPVAIKVLRENTSPKANKEILDEAYVMAGVDSPYVSRLLGICLTSTVQLVTQLMPYGCLLDHVRENRGRLGSQDLLNWCMQIAKGMSYLEDVRLVHRDLAARNVLVKSPNHVKITDFGLARLLDIDETEYHADGGKVPIKWMALESILRRRFTHQSDVWSYGVTVWELMTFGAKPYDGIPAREIPDLLEKGERLPQPPICTIDVYMIMVKCWMIDSECRPRFRELVSEFSRMARDPQRFVVIQNEDLGPASPLDSTFYRSLLEDDDMGDLVDAEEYLVPQQGGGSLEVLFQGPSSPSGSSMKIEEGKLVIWINGDKGYNGLAEVGKKFEKDTGIKVTVEHPDKLEEKFPQVAATGDGPDIIFWAHDRFGGYAQSGLLAEITPDKAFQDKLYPFTWDAVRYNGKLIAYPIAVEALSLIYNKDLLPNPPKTWEEIPALDKELKAKGKSALMFNLQEPYFTWPLIAADGGYAFKYENGKYDIKDVGVDNAGAKAGLTFLVDLIKNKHMNADTDYSIAEAAFNKGETAMTINGPWAWSNIDTSKVNYGVTVLPTFKGQPSKPFVGVLSAGINAASPNKELAKEFLENYLLTDEGLEAVNKDKPLGAVALKSYEEELAKDPRIAATMENAQKGEIMPNIPQMSAFWYAVRTAVINAASGRQTVDEALKDAQTNSSSSGPSSPSAWSHPQFEKGGGSGGGSGGSSAWSHPQFEK |
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 C: ASN30 THR31 ALA32 TYR49 SER50 PHE53 TYR55 ARG66 HIS91 TYR92 THR93 THR94 D: TYR33 ARG50 TYR52 ASN55 TYR57 ARG59 TRP99 ASP102 GLY103 PHE104 TYR105 B: HIS564 PRO579 GLU580 ASP582 GLN583 LYS591 ASP592 PRO593 PRO594 PHE595 PRO601 SER602 ILE613 LYS615 GLU620 ALA622 GLN624 PRO625 CYS626 |
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)
