4K9E | pdb_00004k9e

Crystal structure of KIT D4D5 fragment in complex with anti-Kit antibodies Fab79D

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
SAbDab Antibody 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)
B [auth H]	d4k9eh_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	(Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
A [auth L]	d4k9el2	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	C1 set domains (antibody constant domain-like)	automated matches	(Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
A [auth L]	d4k9el1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	(Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
A [auth L]	d4k9el3	Artifacts	Tags	Tags	Tags	C-terminal Tags	(Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
C	I-set_13	e4k9eC1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: I-set_13	ECOD (1.6)
C	I-set	e4k9eC2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: I-set	ECOD (1.6)
B [auth H]	V-set_8	e4k9eH2	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 [auth H]	C1-set_1	e4k9eH1	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)
A [auth L]	C1-set_4	e4k9eL1	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 [auth L]	V-set	e4k9eL2	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)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
C	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
B [auth H]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
A [auth L]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
B [auth H]	Heavy Chain	IGHV3	-	mast/stem cell growth factor receptor kit	SAbDab (2025-11-14)
A [auth L]	Light Chain	IGKV1	Kappa	mast/stem cell growth factor receptor kit	SAbDab (2025-11-14)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C	Mast/stem cell growth factor receptor Kit	protein tyrosine kinase activity catalytic activity, acting on a protein kinase activity protein kinase activity transferase activity catalytic activity phosphotransferase activity, alcohol group as acceptor transferase activity, transferring phosphorus-containing groups binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding protein tyrosine kinase activity catalytic activity, acting on a protein kinase activity protein kinase activity transferase activity catalytic activity phosphotransferase activity, alcohol group as acceptor transferase activity, transferring phosphorus-containing groups 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 molecular transducer activity signaling receptor activity stem cell factor receptor activity transmembrane receptor protein tyrosine kinase activity transmembrane receptor protein kinase activity transmembrane signaling receptor activity cation binding metal ion binding protein binding enzyme binding protease binding growth factor binding identical protein binding protein homodimerization activity protein dimerization activity SH2 domain binding protein domain specific binding cytokine binding	cellular response to stimulus immune response-regulating cell surface receptor signaling pathway regulation of biological process regulation of cellular process response to stimulus cell surface receptor signaling pathway signaling immune response biological regulation cell communication Fc receptor signaling pathway immune response-regulating signaling pathway regulation of response to stimulus immune system process cellular response to stimulus immune response-regulating cell surface receptor signaling pathway regulation of biological process regulation of cellular process response to stimulus cell surface receptor signaling pathway signaling immune response biological regulation cell communication Fc receptor signaling pathway immune response-regulating signaling pathway regulation of response to stimulus immune system process regulation of immune response cellular process regulation of immune system process signal transduction multicellular organismal process smooth muscle cell differentiation cellular developmental process regulation of developmental process positive regulation of smooth muscle cell differentiation regulation of smooth muscle cell differentiation positive regulation of biological process regulation of cell differentiation muscle cell differentiation muscle structure development positive regulation of developmental process multicellular organism development vascular associated smooth muscle cell differentiation positive regulation of cell differentiation cell differentiation anatomical structure development positive regulation of cellular process system development developmental process positive regulation of vascular associated smooth muscle cell differentiation regulation of vascular associated smooth muscle cell differentiation positive regulation of muscle cell differentiation vasculature development circulatory system development regulation of muscle cell differentiation lamellipodium assembly plasma membrane bounded cell projection organization cell projection organization plasma membrane bounded cell projection assembly cellular component organization cellular component biogenesis cellular component assembly lamellipodium organization cellular component organization or biogenesis cell projection assembly regulation of cellular component organization positive regulation of cellular component organization pseudopodium assembly positive regulation of cell projection organization positive regulation of cellular component biogenesis regulation of cell projection organization regulation of cell projection assembly regulation of cellular component biogenesis regulation of plasma membrane bounded cell projection assembly positive regulation of pseudopodium assembly regulation of pseudopodium assembly regulation of plasma membrane bounded cell projection organization positive regulation of plasma membrane bounded cell projection assembly pseudopodium organization tongue development sensory organ development animal organ development positive regulation of DNA-binding transcription factor activity RNA metabolic process regulation of primary metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process positive regulation of molecular function nucleic acid biosynthetic process DNA-templated transcription regulation of RNA metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of biosynthetic process primary metabolic process regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process regulation of molecular function regulation of gene expression biosynthetic process regulation of DNA-binding transcription factor activity metabolic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription macromolecule metabolic process regulation of metabolic process myeloid leukocyte differentiation hemopoiesis cell development myeloid cell differentiation mast cell differentiation leukocyte differentiation regulation of immune effector process positive regulation of leukocyte mediated immunity positive regulation of macromolecule biosynthetic process positive regulation of metabolic process dendritic cell cytokine production cytokine production leukocyte mediated immunity positive regulation of macromolecule metabolic process positive regulation of immune system process regulation of cytokine production involved in immune response immune effector process regulation of leukocyte mediated immunity positive regulation of production of molecular mediator of immune response positive regulation of multicellular organismal process regulation of production of molecular mediator of immune response positive regulation of cytokine production positive regulation of dendritic cell cytokine production positive regulation of biosynthetic process regulation of dendritic cell cytokine production regulation of cytokine production regulation of multicellular organismal process positive regulation of immune effector process cytokine production involved in immune response production of molecular mediator of immune response positive regulation of gene expression positive regulation of cytokine production involved in immune response hematopoietic stem cell migration cell migration cell motility cell activation mononuclear cell differentiation lymphocyte activation lymphocyte differentiation leukocyte activation T cell activation T cell differentiation immature B cell differentiation B cell activation B cell differentiation negative regulation of programmed cell death negative regulation of cellular process negative regulation of biological process regulation of programmed cell death cell death programmed cell death embryo development embryonic hemopoiesis embryonic organ development maintenance of cell number stem cell population maintenance cell population proliferation leukocyte proliferation mast cell proliferation reproductive process developmental process involved in reproduction programmed cell death involved in cell development ectopic germ cell programmed cell death somatic stem cell population maintenance epithelium migration tissue migration ameboidal-type cell migration epithelial cell migration melanocyte migration sexual reproduction multicellular organismal reproductive process germ cell migration gamete generation pigment cell differentiation pigmentation developmental pigmentation melanocyte differentiation negative regulation of developmental process myeloid progenitor cell differentiation hematopoietic progenitor cell differentiation positive regulation of cell population proliferation regulation of cell population proliferation detection of external stimulus system process nervous system process detection of mechanical stimulus involved in sensory perception of sound response to mechanical stimulus response to external stimulus detection of mechanical stimulus involved in sensory perception sensory perception of mechanical stimulus detection of abiotic stimulus detection of stimulus sensory perception detection of mechanical stimulus response to abiotic stimulus detection of stimulus involved in sensory perception sensory perception of sound establishment of organelle localization regulated exocytosis cellular localization transport cell activation involved in immune response leukocyte degranulation myeloid leukocyte activation myeloid leukocyte mediated immunity vesicle-mediated transport localization secretion by cell organelle localization leukocyte activation involved in immune response establishment of localization in cell mast cell activation mast cell mediated immunity secretion vacuolar localization export from cell mast cell degranulation establishment of localization myeloid cell activation involved in immune response mast cell activation involved in immune response exocytosis lysosome localization epithelial cell proliferation positive regulation of locomotion regulation of cell motility positive regulation of cell migration regulation of locomotion positive regulation of cell motility regulation of cell migration locomotion defense response response to stress inflammatory response intracellular signal transduction gonad development reproductive system development sex differentiation male gonad development male sex differentiation development of primary male sexual characteristics development of primary sexual characteristics reproductive structure development response to cytokine cytokine-mediated signaling pathway response to peptide response to chemical cellular response to cytokine stimulus spermatogenesis male gamete generation positive regulation of mast cell proliferation regulation of leukocyte proliferation regulation of mast cell proliferation positive regulation of leukocyte proliferation organelle organization actin cytoskeleton organization actin filament-based process cytoskeleton organization protein phosphorylation protein autophosphorylation phosphorylation macromolecule modification phosphate-containing compound metabolic process protein metabolic process protein modification process phosphorus metabolic process negative regulation of reproductive process regulation of reproductive process spermatid development spermatid differentiation cellular process involved in reproduction in multicellular organism germ cell development female gonad development female sex differentiation development of primary female sexual characteristics ovarian follicle development cell chemotaxis chemotaxis cellular response to chemical stimulus taxis positive regulation of myeloid leukocyte cytokine production involved in immune response mast cell cytokine production myeloid leukocyte cytokine production regulation of mast cell cytokine production positive regulation of mast cell cytokine production homeostatic process erythrocyte differentiation multicellular organismal-level homeostasis homeostasis of number of cells myeloid cell homeostasis erythrocyte homeostasis cellular response to stem cell factor stimulus cell surface receptor protein tyrosine kinase signaling pathway Kit signaling pathway enzyme-linked receptor protein signaling pathway response to stem cell factor membrane lipid metabolic process glycosphingolipid metabolic process glycolipid metabolic process liposaccharide metabolic process carbohydrate derivative metabolic process sphingolipid metabolic process lipid metabolic process positive regulation of smooth muscle contraction regulation of system process intestine smooth muscle contraction regulation of gastro-intestinal system smooth muscle contraction positive regulation of small intestine smooth muscle contraction smooth muscle contraction regulation of smooth muscle contraction regulation of small intestine smooth muscle contraction small intestine smooth muscle contraction gastro-intestinal system smooth muscle contraction phasic smooth muscle contraction muscle contraction muscle system process regulation of muscle system process positive regulation of gastro-intestinal system smooth muscle contraction regulation of muscle contraction positive regulation of muscle contraction megakaryocyte differentiation megakaryocyte development myeloid cell development erythropoietin-mediated signaling pathway response to erythropoietin cellular response to erythropoietin digestive system development tube development digestive tract development positive regulation of cell communication regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction positive regulation of signal transduction regulation of 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 positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction regulation of cell communication phosphatidylinositol 3-kinase/protein kinase B signal transduction positive regulation of signaling response to light stimulus learning learning or memory visual learning visual behavior cognition associative learning behavior response to radiation mast cell migration leukocyte migration mast cell chemotaxis myeloid leukocyte migration leukocyte chemotaxis lymphoid progenitor cell differentiation regulation of cell shape cell morphogenesis regulation of cell morphogenesis anatomical structure morphogenesis regulation of biological quality regulation of anatomical structure morphogenesis cell adhesion cell-cell adhesion epithelial cell-cell adhesion melanocyte adhesion positive regulation of MAPK cascade regulation of MAPK cascade MAPK cascade positive regulation of phosphorylation positive regulation of phosphate metabolic process peptidyl-amino acid modification positive regulation of protein phosphorylation tyrosine phosphorylation of STAT protein positive regulation of phosphorus metabolic process regulation of protein metabolic process regulation of phosphorus metabolic process cell surface receptor signaling pathway via STAT regulation of protein modification process regulation of protein phosphorylation positive regulation of protein metabolic process peptidyl-tyrosine modification positive regulation of peptidyl-tyrosine phosphorylation positive regulation of protein modification process regulation of tyrosine phosphorylation of STAT protein regulation of peptidyl-tyrosine phosphorylation positive regulation of tyrosine phosphorylation of STAT protein regulation of phosphorylation peptidyl-tyrosine phosphorylation cell surface receptor signaling pathway via JAK-STAT pyloric antrum smooth muscle contraction regulation of pyloric antrum smooth muscle contraction stomach smooth muscle contraction stomach pylorus smooth muscle contraction distal stomach smooth muscle contraction positive regulation of pyloric antrum smooth muscle contraction positive regulation of receptor signaling pathway via STAT positive regulation of receptor signaling pathway via JAK-STAT regulation of receptor signaling pathway via JAK-STAT regulation of receptor signaling pathway via STAT colon smooth muscle contraction regulation of colon smooth muscle contraction positive regulation of colon smooth muscle contraction positive regulation of nervous system development regulation of long-term neuronal synaptic plasticity modulation of chemical synaptic transmission regulation of neurogenesis regulation of cell development regulation of nervous system development neurogenesis synaptic signaling positive regulation of long-term neuronal synaptic plasticity positive regulation of neurogenesis regulation of neuronal synaptic plasticity regulation of synaptic plasticity trans-synaptic signaling regulation of multicellular organismal development positive regulation of cell development cell-cell signaling nervous system development chemical synaptic transmission regulation of trans-synaptic signaling anterograde trans-synaptic signaling Notch signaling pathway regulation of Notch signaling pathway positive regulation of Notch signaling pathway response to metal ion response to cadmium ion stem cell differentiation	cell-cell junction cellular anatomical structure anchoring junction cell junction protein-containing complex receptor complex extracellular region extracellular space acrosomal vesicle membrane-bounded organelle intracellular anatomical structure intracellular vesicle intracellular membrane-bounded organelle endomembrane system cell-cell junction cellular anatomical structure anchoring junction cell junction protein-containing complex receptor complex extracellular region extracellular space acrosomal vesicle membrane-bounded organelle intracellular anatomical structure intracellular vesicle intracellular membrane-bounded organelle endomembrane system intracellular organelle cytoplasmic vesicle organelle secretory granule secretory vesicle cytoplasm vesicle cell periphery plasma membrane membrane nucleus membrane-enclosed lumen intracellular membraneless organelle nucleolus intracellular organelle lumen organelle lumen fibrillar center membraneless organelle nuclear lumen cell surface external side of plasma membrane side of membrane cytoplasmic side of plasma membrane cytoplasmic side of membrane
B [auth H]	heavy chain	-	-	-
A [auth L]	light chain	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C	IPR001824	Tyrosine-protein kinase, receptor class III, conserved site	Conserved Site
C	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
C	IPR020635	Tyrosine-protein kinase, catalytic domain	Domain
C	IPR027263	Mast/stem cell growth factor receptor	Family
C	IPR000719	Protein kinase domain	Domain
C	IPR003599	Immunoglobulin domain subtype	Domain
C	IPR013151	Immunoglobulin-like beta-sandwich domain	Domain
C	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
C	IPR007110	Immunoglobulin-like domain	Domain
C	IPR017441	Protein kinase, ATP binding site	Binding Site
C	IPR001245	Serine-threonine/tyrosine-protein kinase, catalytic domain	Domain
C	IPR008266	Tyrosine-protein kinase, active site	Active Site
C	IPR003598	Immunoglobulin subtype 2	Domain
C	IPR011009	Protein kinase-like domain superfamily	Homologous Superfamily
C	IPR050122	Receptor Tyrosine Kinase	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
C	Pharos: P10721	gastrointestinal stromal tumor systemic mastocytosis mastocytosis piebaldism acute myeloid leukemia testicular germ cell tumor non-small cell lung carcinoma small cell lung carcinoma breast cancer breast carcinoma cancer acute promyelocytic leukemia indolent systemic mastocytosis Neoplasm Recurrence, Local lung disease gastrointestinal stromal tumor systemic mastocytosis mastocytosis piebaldism acute myeloid leukemia testicular germ cell tumor non-small cell lung carcinoma small cell lung carcinoma breast cancer breast carcinoma cancer acute promyelocytic leukemia indolent systemic mastocytosis Neoplasm Recurrence, Local lung disease malignant mesothelioma cutaneous solitary mastocytoma Ewing sarcoma aggressive systemic mastocytosis thymic carcinoma pseudoxanthomatous diffuse cutaneous mastocytosis maculopapular cutaneous mastocytosis congenital anomaly of kidney and urinary tract malignant ependymoma skin cancer cutaneous lupus erythematosus skin neoplasm cystic fibrosis digestive system disease medullary thyroid gland carcinoma telangiectasia macularis eruptiva perstans idiopathic hypereosinophilic syndrome myeloproliferative neoplasm atypical teratoid rhabdoid tumor isolated bone marrow mastocytosis osteosarcoma thymus neoplasm leiomyoma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia bullous diffuse cutaneous mastocytosis tuberculosis lung carcinoma pilocytic astrocytoma chronic eosinophilic leukemia lymphatic system disease psoriasis colorectal adenocarcinoma schwannoma connective tissue disease malignant glioma skin disease cutaneous melanoma MALT lymphoma small cell carcinoma mast cell leukemia subependymal giant cell astrocytoma endometrial carcinoma medulloblastoma adrenal cortex carcinoma systemic mastocytosis with an associated clonal hematologic non-mast cell lineage disease glioblastoma mucosal melanoma anemia tenosynovial giant cell tumor kidney disease ovarian cancer thyroid gland follicular carcinoma lung adenocarcinoma ulcerative colitis pituitary cancer lymphoplasmacytic lymphoma renal cell carcinoma congenital anemia malignant colon neoplasm seminoma dermatofibrosarcoma protuberans acute myelomonocytic leukemia M4 systemic lupus erythematosus melanoma hepatocellular carcinoma astrocytic tumor testicular cancer intellectual disability bone marrow disease large cell medulloblastoma pancreatic intraductal papillary-mucinous neoplasm peripheral primitive neuroectodermal tumor breast disease thyroid gland papillary carcinoma lung cancer

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.