Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 1588 |
| PDBID: | 5MY6 |
| Chains: | B_A |
| Organism: | Homo sapiens, Camelus dromedarius |
| Method: | XRD |
| Resolution (Å): | 2.25 |
| Reference: | 10.1158/1078-0432.CCR-17-0310 |
| Antibody | |
| Antibody: | 2Rs15d Nanobody |
| Antibody mutation: | No |
| INN (Clinical Trial): | |
| Antigen | |
| Antigen: | Receptor tyrosine-protein kinase erbB-2 |
| Antigen mutation: | No |
| Durg Target: | P04626 |
Sequence information
Antibody
Chain: B
Mutation: NULL
| >5MY6_B|Chain B|Nanobody 2Rs15d|Camelus dromedarius (9838) QVQLQESGGGSVQAGGSLKLTCAASGYIFNSCGMGWYRQSPGRERELVSRISGDGDTWHKESVKGRFTISQDNVKKTLYLQMNSLKPEDTAVYFCAVCYNLETYWGQGTQVTVSS |
Antigen
Chain: A
Mutation: NULL
| >5MY6_A|Chain A|Receptor tyrosine-protein kinase erbB-2|Homo sapiens (9606) QVCTGTDMKLRLPASPETHLDMLRHLYQGCQVVQGNLELTYLPTNASLSFLQDIQEVQGYVLIAHNQVRQVPLQRLRIVRGTQLFEDNYALAVLDNGDPLNNTTPVTGASPGGLRELQLRSLTEILKGGVLIQRNPQLCYQDTILWKDIFHKNNQLALTLIDTNRSRACHPCSPMCKGSRCWGESSEDCQSLTRTVCAGGCARCKGPLPTDCCHEQCAAGCTGPKHSDCLACLHFNHSGICELHCPALVTYNTDTFESMPNPEGRYTFGASCVTACPYNYLSTDVGSCTLVCPLHNQEVTAEDGTQRCEKCSKPCARVCYGLGMEHLREVRAVTSANIQEFAGCKKIFGSLAFLPESFDGDPASNTAPLQPEQLQVFETLEEITGYLYISAWPDSLPDLSVFQNLQVIRGRILHNGAYSLTLQGLGISWLGLRSLRELGSGLALIHHNTHLCFVHTVPWDQLFRNPHQALLHTANRPEDECVGEGLACHQLCARGHCWGPGPTQCVNCSQFLRGQECVEECRVLQGLPREYVNARHCLPCHPECQPQNGSVTCFGPEADQCVACAHYKDPPFCVARCPSGVKPDLSYMPIWKFPDEEGACQPCPINCTHSCVDLDDKGCPAE |
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 B: SER31 CYS32 GLY33 MET34 GLY35 TYR37 GLU44 ARG45 LEU47 ARG50 SER52 GLY53 ASP54 TRP58 ALA96 CYS98 ASN100 LEU101 GLU102 THR103 TRP105 A: GLU109 ASP110 ASN111 TYR112 LYS150 GLN156 ARG157 LYS170 PHE173 HIS174 LYS175 ASN177 GLN178 LEU179 ALA180 LEU181 THR182 LEU183 ARG217 |
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)
