Annotations: 9IUT

Crystal structure of cancer-specific anti-HER2 antibody H2Mab-250 in complex with epitope peptide

External Resource: Annotation

Domain Annotation: ECOD Classification
SAbDab Antibody Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
D	p450	e9iutD1	A: alpha arrays	X: Hypothetical protein YqbG-like	H: Hypothetical protein YqbG-like	T: Hypothetical protein YqbG-like	F: p450	ECOD (v295.2)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
A, D	Heavy Chain	IGHV5	-	h2mab-250 epitope peptide	SAbDab (2026-08-28)
B, E	Light Chain	IGKV1	Kappa	h2mab-250 epitope peptide	SAbDab (2026-08-28)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, D	H2Mab-250 VH(S112C)-SARAH	-	-	-
C, F	H2Mab-250 epitope peptide	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 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 to postsynaptic specialization membrane protein localization to postsynaptic membrane protein localization to cell periphery cellular localization 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 macromolecule localization protein localization to organelle protein localization to postsynaptic specialization membrane protein localization to postsynaptic membrane protein localization to cell periphery cellular localization 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 macromolecule localization protein localization to organelle cellular process protein localization to postsynapse intracellular protein localization regulation of biological quality protein localization to cell junction receptor localization to synapse multicellular organismal process regulation of developmental process angiogenesis regulation of vasculature development multicellular organism development tube morphogenesis anatomical structure development regulation of multicellular organismal process regulation of anatomical structure morphogenesis blood vessel development system development developmental process regulation of multicellular organismal development regulation of biological process blood vessel morphogenesis tube development vasculature development circulatory system development anatomical structure morphogenesis regulation of angiogenesis anatomical structure formation involved in morphogenesis animal gross anatomical part developmental process 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 RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process biosynthetic process metabolic process macromolecule metabolic process ERBB2-ERBB3 signaling pathway ERBB3 signaling pathway positive regulation of cell communication positive regulation of signal transduction positive regulation of biological process regulation of signal transduction intracellular signal transduction positive regulation of response to stimulus positive regulation of JNK cascade regulation of intracellular signal transduction JNK cascade intracellular signaling cassette positive regulation of cellular process regulation of signaling positive regulation of MAPK cascade regulation of JNK cascade positive regulation of intracellular signal transduction regulation of MAPK cascade regulation of response to stimulus MAPK cascade regulation of cell communication positive regulation of signaling epidermal growth factor receptor signaling pathway protein phosphorylation phosphorylation macromolecule modification phosphate-containing compound metabolic process protein metabolic process protein modification process ERK1 and ERK2 cascade regulation of ERK1 and ERK2 cascade ERBB2-EGFR signaling pathway 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 establishment of protein localization to membrane regulation of establishment of protein localization establishment of localization protein targeting to membrane regulation of cellular localization regulation of protein targeting 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 phosphatidylinositol 3-kinase/protein kinase B signal transduction negative regulation of programmed cell death regulation of apoptotic process negative regulation of biological process regulation of programmed cell death cell death negative regulation of apoptotic process negative regulation of cellular process apoptotic process programmed cell death cellular developmental process peripheral nervous system development cell development nervous system development glial cell development neurogenesis Schwann cell development gliogenesis glial cell differentiation cell differentiation Schwann cell differentiation small GTPase-mediated signal transduction regulation of small GTPase mediated signal transduction Rho protein 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 cell population proliferation positive regulation of epithelial cell proliferation regulation of cell population proliferation regulation of epithelial cell proliferation epithelial cell proliferation generation of neurons neuron differentiation cell adhesion positive regulation of cell adhesion regulation of cell adhesion positive regulation of protein metabolic process positive regulation of translation protein biosynthetic process 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 translation regulation of gene expression positive regulation of gene expression regulation of translation regulation of macromolecule biosynthetic process regulation of metabolic process 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 positive regulation of protein phosphorylation positive regulation of MAP kinase activity regulation of molecular function positive regulation of kinase activity regulation of kinase activity regulation of protein serine/threonine kinase activity 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 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 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 regulation of transcription by RNA polymerase I positive regulation of RNA metabolic process positive regulation of RNA biosynthetic process regulation of DNA-templated transcription cellular response to epidermal growth factor stimulus response to epidermal growth factor regulation of microtubule-based process microtubule-based process	cell periphery postsynapse cellular anatomical structure postsynaptic membrane synapse cell junction membrane plasma membrane plasma membrane region synaptic membrane intracellular anatomical structure cytoplasm cytosol protein-containing complex cell periphery postsynapse cellular anatomical structure postsynaptic membrane synapse cell junction membrane plasma membrane plasma membrane region synaptic membrane intracellular anatomical structure cytoplasm cytosol protein-containing complex plasma membrane protein complex plasma membrane signaling receptor complex membrane protein complex signaling receptor complex ERBB3:ERBB2 complex presynapse presynaptic 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
B, E	H2Mab-250 VL-SARAH(S37C)	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

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

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
C, F	: 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 chromophobe renal cell carcinoma glioma malignant pancreatic neoplasm 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 ependymoma subependymoma biliary tract neoplasm 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 lung adenocarcinoma benign neoplasm of stomach systemic lupus erythematosus bipolar disorder 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 endometriosis stomach carcinoma in situ lung benign neoplasm bile duct cancer breast adenocarcinoma breast fibroadenoma gallbladder neoplasm

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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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.