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Entry information

Complex
AACDB_ID: 2595
PDBID: 6OGE
Chains: ED_A
Organism: Homo sapiens
Method: EM
Resolution (Å): 4.36
Reference: 10.1371/journal.pone.0216095
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; P04626;

Sequence information

Antibody

Heavy Chain: E
Mutation: NULL

>6OGE_E|Chain E|Trastuzumab FAB HEAVY CHAIN|Homo sapiens (9606)
EVQLVESGGGLVQPGGSLRLSCAASGFNIKDTYIHWVRQAPGKGLEWVARIYPTNGYTRYADSVKGRFTISADTSKNTAYLQMNSLRAEDTAVYYCSRWGGDGFYAMDYWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEP

Light Chain: D
Mutation: NULL

>6OGE_D|Chain D|Trastuzumab FAB LIGHT CHAIN|Homo sapiens (9606)
DIQMTQSPSSLSASVGDRVTITCRASQDVNTAVAWYQQKPGKAPKLLIYSASFLYSGVPSRFSGSRSGTDFTLTISSLQPEDFATYYCQQHYTTPPTFGQGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Antigen

Chain: A
Mutation: NULL

>6OGE_A|Chain A|Receptor tyrosine-protein kinase erbB-2|Homo sapiens (9606)
TQVCTGTDMKLRLPASPETHLDMLRHLYQGCQVVQGNLELTYLPTNASLSFLQDIQEVQGYVLIAHNQVRQVPLQRLRIVRGTQLFEDNYALAVLDNGDPLNNTTPVTGASPGGLRELQLRSLTEILKGGVLIQRNPQLCYQDTILWKDIFHKNNQLALTLIDTNRSRACHPCSPMCKGSRCWGESSEDCQSLTRTVCAGGCARCKGPLPTDCCHEQCAAGCTGPKHSDCLACLHFNHSGICELHCPALVTYNTDTFESMPNPEGRYTFGASCVTACPYNYLSTDVGSCTLVCPLHNQEVTAEDGTQRCEKCSKPCARVCYGLGMEHLREVRAVTSANIQEFAGCKKIFGSLAFLPESFDGDPASNTAPLQPEQLQVFETLEEITGYLYISAWPDSLPDLSVFQNLQVIRGRILHNGAYSLTLQGLGISWLGLRSLRELGSGLALIHHNTHLCFVHTVPWDQLFRNPHQALLHTANRPEDECVGEGLACHQLCARGHCWGPGPTQCVNCSQFLRGQECVEECRVLQGLPREYVNARHCLPCHPECQPQNGSVTCFGPEADQCVACAHYKDPPFCVARCPSGVKPDLSYMPIWKFPDEEGACQPCPINCTHSCVDLDDKGCPA

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: ASN30 THR31 ALA32 TYR49 SER50 PHE53 TYR55 SER56 HIS91 TYR92 THR93 THR94

E: VAL2 GLY26 PHE27 ASN28 THR32 TYR33 ARG50 ILE51 TYR52 ASN55 TYR57 ARG59 ARG98 TRP99 GLY100 GLY101 ASP102 GLY103 TYR105 TYR109

A: LEU561 PRO579 GLU580 ASP582 GLN583 LYS591 ASP592 PRO593 PRO594 PHE595 PRO601 PRO606 ASP607 LEU608 TYR610 PRO612 LYS615 ASP618 GLU620 ALA622 GLN624 PRO625 CYS626 PRO627

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)

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