1N8Z

Crystal structure of extracellular domain of human HER2 complexed with Herceptin Fab

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
IMGT Antibody Annotation
SAbDab Antibody Annotation
Thera-SAbDab Antibody Annotation
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d1n8za1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	Immunoglobulin light chain kappa variable domain, VL-kappa	mouse/human (Mus musculus ) [TaxId: 10090 ], mouse/human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d1n8za2	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	C1 set domains (antibody constant domain-like)	Immunoglobulin light chain kappa constant domain, CL-kappa	mouse/human (Mus musculus ) [TaxId: 10090 ], mouse/human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d1n8zb1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	Immunoglobulin heavy chain variable domain, VH	mouse/human (Mus musculus ) [TaxId: 10090 ], mouse/human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d1n8zb2	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	C1 set domains (antibody constant domain-like)	Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma	mouse/human (Mus musculus ) [TaxId: 10090 ], mouse/human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d1n8zc1	Alpha and beta proteins (a/b)	Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)	L domain-like	L domain	Protooncoprotein Her2 extracellular domain	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d1n8zc3	Small proteins	Knottins (small inhibitors, toxins, lectins)	Growth factor receptor domain	Growth factor receptor domain	Protooncoprotein Her2 extracellular domain	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
C	SCOP2 Family	L domain	8031312	4003546	SCOP2 (2022-06-29)
C	SCOP2 Family	L domain	8031313	4003546	SCOP2 (2022-06-29)
C	SCOP2 Family	Growth factor receptor domain	8031314	4003193	SCOP2 (2022-06-29)
C	SCOP2 Family	Growth factor receptor domain	8031316	4003193	SCOP2 (2022-06-29)
C	SCOP2 Superfamily	L domain-like	8043690	3001010	SCOP2 (2022-06-29)
C	SCOP2 Superfamily	L domain-like	8043691	3001010	SCOP2 (2022-06-29)
C	SCOP2 Superfamily	Growth factor receptor domain-like	8043692	3000398	SCOP2 (2022-06-29)
C	SCOP2 Superfamily	Growth factor receptor domain-like	8043694	3000398	SCOP2 (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	C1-set_4	e1n8zA2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C1-set_4	ECOD (1.6)
A	V-set	e1n8zA1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set	ECOD (1.6)
B	V-set_8	e1n8zB1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_8	ECOD (1.6)
B	C1-set_1	e1n8zB2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C1-set_1	ECOD (1.6)
C	Recep_L_domain	e1n8zC1	A: beta duplicates or obligate multimers	X: Single-stranded right-handed beta-helix	H: Leucine-rich repeats (From Topology)	T: Leucine-rich repeats	F: Recep_L_domain	ECOD (1.6)
C	GF_recep_IV	e1n8zC4	A: few secondary structure elements	X: EGF-like	H: Growth factor receptor domain (From Topology)	T: Growth factor receptor domain	F: GF_recep_IV	ECOD (1.6)
C	Furin-like	e1n8zC3	A: few secondary structure elements	X: EGF-like	H: Growth factor receptor domain (From Topology)	T: Growth factor receptor domain	F: Furin-like	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
B	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
C	3.80.20.20	Alpha Beta	Alpha-Beta Horseshoe	24 nucleotide stem-loop, u2 snrnp hairpin iv. U2 a'	Chain A	CATH (4.3.0)
C	2.10.220.10	Mainly Beta	Ribbon	Hormone Receptor, Insulin-like Growth Factor Receptor 1	Chain A domain 2	CATH (4.3.0)

IMGT Antibody Annotation IMGT Database Homepage

Chain	Protein Name	Description	Organism Name	Gene Allele Name(s)	Domain Name(s)	Receptor Type	Receptor Description	Provenance Source
A	4D5-humanized variant 8 Fab, Herceptin Fab	L-KAPPA	Humanized (humanized)	IGKV1-3901, IGKV1D-3901, IGKJ101, IGKC01	V-DOMAIN V-KAPPA, C-DOMAIN C-KAPPA	IG	FAB-GAMMA-1_KAPPA	IMGT (202450-0)
B	4D5-humanized variant 8 Fab, Herceptin Fab	VH-CH1	Humanized (humanized)	IGHV3-6601, IGHV3-6602, IGHV3-6604, IGHJ401, IGHJ402, IGHJ403, IGHG101, IGHG102, IGHG1*04	V-DOMAIN VH, C-DOMAIN CH1	IG	FAB-GAMMA-1_KAPPA	IMGT (202450-0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
A	Light Chain	IGKV1	Kappa	receptor protein-tyrosine kinase erbb-2	SAbDab (2024-12-20)
B	Heavy Chain	IGHV3	-	receptor protein-tyrosine kinase erbb-2	SAbDab (2024-12-20)

Thera-SAbDab Antibody Annotation Thera-SAbDab Database Homepage

Chain	Name	Target	Provenance Source
A	Cinrebafusp	ERBB2/CD340/HER2, SIRPA, CD3E	Therapeutic SAbDab (2024-12-20)
B	Caxmotabart	ERBB2/CD340/HER2, CD3E, SIRPA	Therapeutic SAbDab (2024-12-20)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
C	PF00757	Furin-like cysteine rich region (Furin-like)	Furin-like cysteine rich region	-	Domain
C	PF01030	Receptor L domain (Recep_L_domain)	Receptor L domain	-	Repeat
C	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	Herceptin Fab (antibody) - light chain	-	-	-
B	Herceptin Fab (antibody) - heavy chain	-	-	-
C	Receptor protein-tyrosine kinase erbB-2	molecular transducer activity coreceptor activity signaling receptor activity RNA polymerase I core binding RNA polymerase binding protein binding binding RNA polymerase core enzyme binding enzyme binding catalytic activity, acting on a protein kinase activity protein kinase activity transferase activity phosphotransferase activity, alcohol group as acceptor molecular transducer activity coreceptor activity signaling receptor activity RNA polymerase I core binding RNA polymerase binding protein binding binding RNA polymerase core enzyme binding enzyme binding catalytic activity, acting on a protein kinase activity protein kinase activity transferase activity phosphotransferase activity, alcohol group as acceptor transferase activity, transferring phosphorus-containing groups protein tyrosine kinase activity transmembrane receptor protein tyrosine kinase activity transmembrane receptor protein kinase activity transmembrane signaling receptor activity catalytic activity adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding protein tyrosine kinase binding kinase binding signaling receptor binding receptor tyrosine kinase binding protein kinase binding identical protein binding protein heterodimerization activity protein dimerization activity ErbB-3 class receptor binding	protein localization protein localization to postsynaptic specialization membrane cellular localization protein localization to postsynaptic membrane protein localization to cell periphery protein localization to synapse biological regulation 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 protein localization protein localization to postsynaptic specialization membrane cellular localization protein localization to postsynaptic membrane protein localization to cell periphery protein localization to synapse biological regulation 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 cellular process protein localization to postsynapse regulation of biological quality protein localization to cell junction receptor localization to synapse developmental process multicellular organismal process regulation of multicellular organismal development regulation of biological process regulation of developmental process blood vessel morphogenesis tube development angiogenesis vasculature development regulation of vasculature development circulatory system development multicellular organism development anatomical structure morphogenesis tube morphogenesis regulation of angiogenesis anatomical structure development anatomical structure formation involved in morphogenesis regulation of multicellular organismal process regulation of anatomical structure morphogenesis blood vessel development system development heart development animal organ development cellular response to stimulus ERBB2 signaling pathway ERBB4 signaling pathway regulation of cellular process cell surface receptor signaling pathway response to stimulus signaling cell surface receptor protein tyrosine kinase signaling pathway cell communication ERBB signaling pathway signal transduction enzyme-linked receptor protein signaling pathway ERBB2-ERBB4 signaling pathway cell population proliferation 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 hemopoiesis cell activation immature T cell proliferation immune system process mononuclear cell proliferation leukocyte differentiation ERBB2-ERBB3 signaling pathway ERBB3 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 regulation of leukocyte cell-cell adhesion negative regulation of lymphocyte differentiation 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 regulation of cell-cell adhesion negative regulation of cell differentiation 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 regulation of signaling regulation of signal transduction regulation of MAPK cascade intracellular signal transduction regulation of intracellular signal transduction regulation of response to stimulus intracellular signaling cassette MAPK cascade regulation of cell communication ERK1 and ERK2 cascade regulation of ERK1 and ERK2 cascade epidermal growth factor receptor signaling pathway ERBB2-EGFR signaling pathway regulation of localization establishment of protein localization regulation of protein localization protein targeting positive regulation of biological process positive regulation of establishment of protein localization regulation of protein targeting to membrane regulation of protein localization to membrane positive regulation of cellular process 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 regulation of growth regulation of cellular component organization growth positive regulation of cell growth regulation of cell growth cell growth cellular component organization positive regulation of growth cellular component organization or biogenesis neurogenesis nervous system development central nervous system development gliogenesis oligodendrocyte differentiation glial cell differentiation phosphatidylinositol 3-kinase/protein kinase B signal transduction 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 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 differentiation neuron projection morphogenesis plasma membrane bounded cell projection organization axon guidance axon development cell morphogenesis involved in neuron differentiation generation of neurons neuron projection guidance neuron development positive regulation of cell communication small GTPase-mediated signal transduction positive regulation of signal transduction regulation of small GTPase mediated signal transduction Rho protein signal transduction positive regulation of response to stimulus positive regulation of intracellular signal transduction regulation of Rho protein signal transduction positive regulation of Rho protein signal transduction positive regulation of small GTPase mediated signal transduction positive regulation of signaling positive regulation of cell population proliferation positive regulation of epithelial cell proliferation regulation of epithelial cell proliferation epithelial cell proliferation positive regulation of cell adhesion positive regulation of protein metabolic process positive regulation of translation positive regulation of macromolecule biosynthetic process regulation of primary metabolic process post-transcriptional regulation of gene expression positive regulation of metabolic process positive regulation of biosynthetic process positive regulation of macromolecule metabolic process regulation of biosynthetic process regulation of protein metabolic process regulation of macromolecule metabolic process gene expression translation macromolecule biosynthetic process regulation of gene expression biosynthetic process positive regulation of gene expression regulation of translation regulation of macromolecule biosynthetic process regulation of metabolic process peptidyl-tyrosine modification peptidyl-amino acid modification peptidyl-tyrosine phosphorylation positive regulation of phosphorylation regulation of catalytic activity regulation of transferase activity positive regulation of phosphate metabolic process regulation of MAP kinase activity positive regulation of protein serine/threonine kinase activity regulation of phosphate 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 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 protein modification process regulation of protein phosphorylation 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 phosphorylation semaphorin-plexin signaling pathway 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 nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process DNA-templated transcription regulation of RNA metabolic 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 positive regulation of nucleobase-containing compound metabolic process regulation of transcription by RNA polymerase I nucleobase-containing compound biosynthetic process nucleic acid metabolic process positive regulation of RNA metabolic process positive regulation of RNA biosynthetic process regulation of DNA-templated transcription myelination axon ensheathment ensheathment of neurons cellular response to epidermal growth factor stimulus response to epidermal growth factor regulation of microtubule-based process microtubule-based process	cellular anatomical structure membrane intracellular anatomical structure cytoplasm cytosol cell periphery protein-containing complex plasma membrane protein complex plasma membrane plasma membrane signaling receptor complex membrane protein complex ERBB3:ERBB2 complex receptor complex presynapse cellular anatomical structure membrane intracellular anatomical structure cytoplasm cytosol cell periphery protein-containing complex plasma membrane protein complex plasma membrane plasma membrane signaling receptor complex membrane protein complex ERBB3:ERBB2 complex receptor complex presynapse synapse cell junction presynaptic membrane plasma membrane region synaptic membrane basal part of cell basal plasma membrane basolateral plasma membrane semaphorin receptor complex neuromuscular junction perinuclear region of cytoplasm endosome membrane membrane-bounded organelle 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 myelin sheath apical part of cell apical plasma membrane ruffle cell leading edge leading edge membrane plasma membrane bounded cell projection cell projection ruffle membrane cell projection membrane 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
C	IPR016245	Tyrosine protein kinase, EGF/ERB/XmrK receptor	Family
C	IPR008266	Tyrosine-protein kinase, active site	Active Site
C	IPR020635	Tyrosine-protein kinase, catalytic domain	Domain
C	IPR000719	Protein kinase domain	Domain
C	IPR036941	Receptor L-domain superfamily	Homologous Superfamily
C	IPR032778	Growth factor receptor domain 4	Domain
C	IPR049328	Epidermal growth factor receptor-like, transmembrane-juxtamembrane segment	Domain
C	IPR006212	Furin-like repeat	Repeat
C	IPR000494	Receptor L-domain	Domain
C	IPR017441	Protein kinase, ATP binding site	Binding Site
C	IPR001245	Serine-threonine/tyrosine-protein kinase, catalytic domain	Domain
C	IPR011009	Protein kinase-like domain superfamily	Homologous Superfamily
C	IPR006211	Furin-like cysteine-rich domain	Domain
C	IPR009030	Growth factor receptor cysteine-rich domain superfamily	Homologous Superfamily
C	IPR050122	Receptor Tyrosine Kinase	Family

Pharos: Disease Associations Pharos Homepage Annotation

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

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.