8Q6J

Atomic structure and conformational variability of the HER2-Trastuzumab-Pertuzumab complex

External Resource: Annotation

Domain Annotation: SCOP2 Classification
SAbDab Antibody Annotation
Thera-SAbDab Antibody Annotation
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
E	SCOP2B Superfamily	L domain-like	8043690	3001010	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Growth factor receptor domain-like	8043692	3000398	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	L domain-like	8043691	3001010	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Growth factor receptor domain-like	8043694	3000398	SCOP2B (2022-06-29)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
A	Light Chain	IGKV1	Kappa	receptor tyrosine-protein kinase erbb-2	SAbDab (2025-03-07)
B	Heavy Chain	IGHV3	-	receptor tyrosine-protein kinase erbb-2	SAbDab (2025-03-07)
C	Light Chain	IGKV1	Kappa	receptor tyrosine-protein kinase erbb-2	SAbDab (2025-03-07)
D	Heavy Chain	IGHV3	-	receptor tyrosine-protein kinase erbb-2	SAbDab (2025-03-07)

Thera-SAbDab Antibody Annotation Thera-SAbDab Database Homepage

Chain	Name	Target	Provenance Source
A	Caxmotabart	ERBB2/CD340/HER2, CD3E, SIRPA, ERBB2/CD340/HER2 (Domain II), ERBB2/CD340/HER2 (Domain IV)	Therapeutic SAbDab (2025-03-07)
B	Caxmotabart	ERBB2/CD340/HER2, SIRPA, CD3E	Therapeutic SAbDab (2025-03-07)
C	Pertuzumab	ERBB2/CD340/HER2	Therapeutic SAbDab (2025-03-07)
D	Anbenitamab	ERBB2/CD340/HER2 (Domain II), ERBB2/CD340/HER2 (Domain IV), ERBB2/CD340/HER2	Therapeutic SAbDab (2025-03-07)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
E	PF00757	Furin-like cysteine rich region (Furin-like)	Furin-like cysteine rich region		Domain
E	PF01030	Receptor L domain (Recep_L_domain)	Receptor L domain	-	Repeat
E	PF14843	Growth factor receptor domain IV (GF_recep_IV)	Growth factor receptor domain IV	This is the fourth extracellular domain of receptor tyrosine protein kinases. Interaction between this domain and the furin-like domain (Pfam:PF00757) regulates the binding of ligands to the receptor L domains (Pfam:PF01030) [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Trastuzumab fab light chain	-	-	-
B	Trastuzumab Fab heavy chain	-	-	-
C	Pertuzumab Fab light chain	-	-	-
D	Pertuzumab Fab heavy chain	-	-	-
E	Receptor tyrosine-protein kinase erbB-2	molecular transducer activity catalytic activity, acting on a protein ephrin receptor activity kinase activity protein kinase activity signaling receptor activity transferase activity phosphotransferase activity, alcohol group as acceptor transferase activity, transferring phosphorus-containing groups transmembrane-ephrin receptor activity protein tyrosine kinase activity transmembrane receptor protein tyrosine kinase activity transmembrane receptor protein kinase activity transmembrane signaling receptor activity catalytic activity molecular transducer activity catalytic activity, acting on a protein ephrin receptor activity kinase activity protein kinase activity signaling receptor activity transferase activity phosphotransferase activity, alcohol group as acceptor transferase activity, transferring phosphorus-containing groups transmembrane-ephrin receptor activity protein tyrosine kinase activity transmembrane receptor protein tyrosine kinase activity transmembrane receptor protein kinase activity transmembrane signaling receptor activity catalytic activity collagen receptor activity protein tyrosine kinase collagen receptor activity GPI-linked ephrin receptor activity protein-hormone receptor activity insulin receptor activity binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding platelet-derived growth factor beta-receptor activity platelet-derived growth factor receptor activity stem cell factor receptor activity brain-derived neurotrophic factor receptor activity neurotrophin receptor activity hepatocyte growth factor receptor activity protein binding signaling receptor binding macrophage colony-stimulating factor receptor activity platelet-derived growth factor alpha-receptor activity vascular endothelial growth factor receptor activity ErbB-3 class receptor binding histone H2AXY142 kinase activity histone modifying activity histone kinase activity histone H2AX kinase activity coreceptor activity RNA polymerase I core binding RNA polymerase binding RNA polymerase core enzyme binding enzyme binding histone H3Y41 kinase activity histone H3 kinase activity placental growth factor receptor activity protein tyrosine kinase binding kinase binding receptor tyrosine kinase binding protein kinase binding insulin-like growth factor receptor activity identical protein binding boss receptor activity epidermal growth factor receptor activity protein heterodimerization activity protein dimerization activity fibroblast growth factor receptor activity	developmental process multicellular organismal process regulation of multicellular organismal development regulation of biological process regulation of developmental process blood vessel morphogenesis tube development biological regulation angiogenesis vasculature development regulation of vasculature development circulatory system development anatomical structure morphogenesis multicellular organism development tube morphogenesis developmental process multicellular organismal process regulation of multicellular organismal development regulation of biological process regulation of developmental process blood vessel morphogenesis tube development biological regulation angiogenesis vasculature development regulation of vasculature development circulatory system development anatomical structure morphogenesis multicellular organism development tube morphogenesis regulation of angiogenesis anatomical structure formation involved in morphogenesis anatomical structure development regulation of multicellular organismal process regulation of anatomical structure morphogenesis blood vessel development system development heart development animal organ development cellular developmental process immature T cell proliferation in thymus cell development mononuclear cell differentiation lymphocyte activation lymphocyte differentiation leukocyte proliferation leukocyte activation T cell differentiation in thymus T cell activation cell differentiation lymphocyte proliferation T cell differentiation T cell proliferation cell population proliferation hemopoiesis cell activation immature T cell proliferation immune system process mononuclear cell proliferation cellular process leukocyte differentiation cellular response to stimulus ERBB2 signaling pathway regulation of cellular process cell surface receptor signaling pathway response to stimulus signaling ERBB2-ERBB3 signaling pathway cell surface receptor protein tyrosine kinase signaling pathway cell communication ERBB signaling pathway ERBB3 signaling pathway signal transduction enzyme-linked receptor protein signaling pathway negative regulation of lymphocyte proliferation regulation of leukocyte differentiation regulation of leukocyte activation negative regulation of biological process regulation of cell activation negative regulation of T cell differentiation in thymus regulation of cell differentiation negative regulation of T cell proliferation regulation of cell development negative regulation of cell adhesion negative regulation of T cell differentiation negative regulation of leukocyte proliferation regulation of immune system process regulation of immature T cell proliferation negative regulation of hemopoiesis regulation of leukocyte proliferation negative regulation of immature T cell proliferation negative regulation of leukocyte differentiation regulation of immature T cell proliferation in thymus negative regulation of T cell activation negative regulation of leukocyte cell-cell adhesion regulation of cell population proliferation negative regulation of cell-cell adhesion negative regulation of lymphocyte differentiation regulation of leukocyte cell-cell adhesion negative regulation of multicellular organismal process negative regulation of leukocyte activation regulation of T cell differentiation in thymus negative regulation of lymphocyte activation leukocyte cell-cell adhesion regulation of T cell differentiation negative regulation of mononuclear cell proliferation cell adhesion cell-cell adhesion negative regulation of cellular process negative regulation of cell differentiation regulation of cell-cell adhesion negative regulation of immature T cell proliferation in thymus regulation of lymphocyte proliferation regulation of lymphocyte differentiation negative regulation of cell population proliferation negative regulation of developmental process regulation of cell adhesion regulation of T cell activation negative regulation of cell activation negative regulation of cell development regulation of T cell proliferation negative regulation of immune system process regulation of hemopoiesis regulation of mononuclear cell proliferation regulation of lymphocyte activation protein phosphorylation phosphorylation primary metabolic process macromolecule modification phosphate-containing compound metabolic process metabolic process protein metabolic process macromolecule metabolic process protein modification process phosphorus metabolic process epidermal growth factor receptor signaling pathway ERBB2-EGFR signaling pathway regulation of growth regulation of cellular component organization growth positive regulation of biological process positive regulation of cell growth regulation of cell growth cell growth cellular component organization positive regulation of growth cellular component organization or biogenesis positive regulation of cellular process neurogenesis nervous system development negative regulation of programmed cell death regulation of apoptotic process regulation of programmed cell death cell death negative regulation of apoptotic process apoptotic process programmed cell death positive regulation of cell communication small GTPase-mediated signal transduction positive regulation of signal transduction regulation of small GTPase mediated signal transduction regulation of signal transduction intracellular signal transduction Rho protein signal transduction positive regulation of response to stimulus regulation of intracellular signal transduction intracellular signaling cassette regulation of signaling positive regulation of intracellular signal transduction regulation of Rho protein signal transduction positive regulation of Rho protein signal transduction regulation of response to stimulus regulation of cell communication positive regulation of small GTPase mediated signal transduction positive regulation of signaling generation of neurons neuron differentiation positive regulation of cell adhesion positive regulation of cell population proliferation positive regulation of phosphorylation regulation of catalytic activity regulation of transferase activity positive regulation of phosphate metabolic process regulation of MAP kinase activity regulation of primary metabolic process positive regulation of protein serine/threonine kinase activity positive regulation of metabolic process regulation of phosphate metabolic process positive regulation of macromolecule metabolic process positive regulation of protein phosphorylation positive regulation of MAP kinase activity positive regulation of phosphorus metabolic process positive regulation of MAPK cascade regulation of protein metabolic process regulation of MAPK cascade regulation of molecular function positive regulation of kinase activity regulation of kinase activity regulation of protein serine/threonine kinase activity regulation of phosphorus metabolic process regulation of metabolic process regulation of protein modification process regulation of protein phosphorylation positive regulation of protein metabolic process positive regulation of molecular function positive regulation of protein modification process positive regulation of protein kinase activity positive regulation of transferase activity positive regulation of catalytic activity regulation of protein kinase activity regulation of macromolecule metabolic process MAPK cascade regulation of phosphorylation cellular response to endogenous stimulus cellular response to growth factor stimulus response to endogenous stimulus response to growth factor wound healing response to stress response to wounding positive regulation of DNA-templated transcription RNA metabolic process positive regulation of macromolecule biosynthetic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process DNA-templated transcription regulation of RNA metabolic process positive regulation of biosynthetic process transcription by RNA polymerase I regulation of nucleobase-containing compound metabolic process positive regulation of transcription by RNA polymerase I regulation of RNA biosynthetic process regulation of biosynthetic process positive regulation of nucleobase-containing compound metabolic process regulation of transcription by RNA polymerase I nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process positive regulation of RNA metabolic process regulation of gene expression biosynthetic process positive regulation of RNA biosynthetic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription cellular response to epidermal growth factor stimulus response to epidermal growth factor protein localization protein localization to postsynaptic specialization membrane cellular localization protein localization to postsynaptic membrane protein localization to cell periphery protein localization to synapse localization within membrane protein localization to membrane protein-containing complex localization neurotransmitter receptor localization to postsynaptic specialization membrane localization regulation of postsynaptic membrane neurotransmitter receptor levels protein localization to organelle cellular macromolecule localization macromolecule localization protein localization to postsynapse regulation of biological quality protein localization to cell junction receptor localization to synapse ERBB4 signaling pathway ERBB2-ERBB4 signaling pathway ERK1 and ERK2 cascade regulation of ERK1 and ERK2 cascade regulation of localization establishment of protein localization regulation of protein localization protein targeting positive regulation of establishment of protein localization regulation of protein targeting to membrane regulation of protein localization to membrane establishment of protein localization to membrane regulation of establishment of protein localization positive regulation of protein localization to membrane establishment of localization protein targeting to membrane regulation of cellular localization regulation of protein targeting positive regulation of protein localization positive regulation of protein targeting to membrane central nervous system development gliogenesis oligodendrocyte differentiation glial cell differentiation phosphatidylinositol 3-kinase/protein kinase B signal transduction peripheral nervous system development glial cell development Schwann cell development Schwann cell differentiation cell junction organization neuromuscular junction development synapse organization axonogenesis cell projection organization motor neuron axon guidance plasma membrane bounded cell projection morphogenesis neuron projection development cell morphogenesis cell projection morphogenesis neuron projection morphogenesis plasma membrane bounded cell projection organization axon guidance axon development cell morphogenesis involved in neuron differentiation neuron projection guidance neuron development positive regulation of epithelial cell proliferation regulation of epithelial cell proliferation epithelial cell proliferation positive regulation of translation post-transcriptional regulation of gene expression translation positive regulation of gene expression regulation of translation peptidyl-tyrosine modification peptidyl-amino acid modification peptidyl-tyrosine phosphorylation semaphorin-plexin signaling pathway myelination axon ensheathment ensheathment of neurons regulation of microtubule-based process microtubule-based process	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol protein-containing complex receptor complex neuromuscular junction synapse cell junction endosome membrane membrane-bounded organelle membrane endosome intracellular vesicle cellular anatomical structure intracellular anatomical structure cytoplasm cytosol protein-containing complex receptor complex neuromuscular junction synapse cell junction endosome membrane membrane-bounded organelle membrane endosome intracellular vesicle intracellular membrane-bounded organelle endomembrane system intracellular organelle cytoplasmic vesicle membrane bounding membrane of organelle vesicle membrane cytoplasmic vesicle organelle vesicle organelle membrane cell periphery apical part of cell plasma membrane plasma membrane region apical plasma membrane ruffle cell leading edge leading edge membrane plasma membrane bounded cell projection cell projection ruffle membrane cell projection membrane basal part of cell basal plasma membrane plasma membrane protein complex plasma membrane signaling receptor complex membrane protein complex ERBB3:ERBB2 complex presynapse presynaptic membrane synaptic membrane basolateral plasma membrane semaphorin receptor complex perinuclear region of cytoplasm myelin sheath nucleus membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen early endosome

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
E	IPR016245	Tyrosine protein kinase, EGF/ERB/XmrK receptor	Family
E	IPR020635	Tyrosine-protein kinase, catalytic domain	Domain
E	IPR000719	Protein kinase domain	Domain
E	IPR032778	Growth factor receptor domain 4	Domain
E	IPR006212	Furin-like repeat	Repeat
E	IPR017441	Protein kinase, ATP binding site	Binding Site
E	IPR001245	Serine-threonine/tyrosine-protein kinase, catalytic domain	Domain
E	IPR009030	Growth factor receptor cysteine-rich domain superfamily	Homologous Superfamily
E	IPR008266	Tyrosine-protein kinase, active site	Active Site
E	IPR036941	Receptor L-domain superfamily	Homologous Superfamily
E	IPR049328	Epidermal growth factor receptor-like, transmembrane-juxtamembrane segment	Domain
E	IPR000494	Receptor L-domain	Domain
E	IPR011009	Protein kinase-like domain superfamily	Homologous Superfamily
E	IPR006211	Furin-like cysteine-rich domain	Domain
E	IPR050122	Receptor Tyrosine Kinase	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
E	Pharos: P04626	lung cancer gastric cancer ovarian cancer Lymphatic Metastasis cholangiocarcinoma prostate cancer medulloblastoma invasive ductal breast carcinoma nasopharyngeal carcinoma breast carcinoma malignant glioma papilloma renal cell carcinoma childhood medulloblastoma head and neck cancer lung cancer gastric cancer ovarian cancer Lymphatic Metastasis cholangiocarcinoma prostate cancer medulloblastoma invasive ductal breast carcinoma nasopharyngeal carcinoma breast carcinoma malignant glioma papilloma renal cell carcinoma childhood medulloblastoma head and neck cancer adenocarcinoma adult medulloblastoma intrahepatic cholangiocarcinoma mixed glioma ductal breast carcinoma in situ ulcerative colitis breast cancer neuroblastoma papillary renal cell carcinoma glioblastoma glioma susceptibility 1 collecting duct carcinoma sarcomatoid renal cell carcinoma melanotic medulloblastoma skin basal cell carcinoma squamous papilloma lung carcinoma gallbladder cancer urinary bladder cancer glioma malignant pancreatic neoplasm chromophobe renal cell carcinoma granular cell carcinoma hereditary diffuse gastric adenocarcinoma medullomyoblastoma with myogenic differentiation esophageal cancer tubular adenocarcinoma malignant colon neoplasm ovarian carcinoma gastric carcinoma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia papillomatosis clear cell renal carcinoma primary biliary cholangitis mammary neoplasms, animal colonic neoplasm marginal zone lymphoma sarcoma melanoma Crohn disease astrocytoma (excluding glioblastoma) skin pigmented basal cell carcinoma liver disease benign colon neoplasm neoplasm of esophagus ependymoma subependymoma biliary tract neoplasm malignant ependymoma non-small cell lung carcinoma ovarian neoplasm gastric neoplasm carcinoma peripheral nervous system disease head and neck carcinoma colorectal adenocarcinoma renal carcinoma cribriform carcinoma inflammatory bowel disease desmoplastic/nodular medulloblastoma atopic eczema lung adenocarcinoma benign neoplasm of stomach systemic lupus erythematosus bipolar disorder lymphoma neutropenia cancer pancreatic ductal adenocarcinoma peripheral neuropathy colonic disease head and neck neoplasm colorectal cancer cribriform carcinoma of breast interstitial cystitis digestive system cancer skin disease leukemia atypical teratoid rhabdoid tumor endometriosis stomach carcinoma in situ lung benign neoplasm bile duct cancer breast adenocarcinoma gallbladder neoplasm breast fibroadenoma

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.