2QJ4 | pdb_00002qj4

A Mechanistic Basis for Converting a Receptor Tyrosine Kinase Agonist to an Antagonist

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
B	d2qj4b1	Small proteins	Hairpin loop containing domain-like	Hairpin loop containing domain-like	Hairpin loop containing domain	automated matches	house mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
B	d2qj4b2	Small proteins	Kringle-like	Kringle-like	Kringle modules	automated matches	house mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
A	d2qj4a1	Small proteins	Hairpin loop containing domain-like	Hairpin loop containing domain-like	Hairpin loop containing domain	automated matches	house mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
A	d2qj4a2	Small proteins	Kringle-like	Kringle-like	Kringle modules	automated matches	house mouse (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)
B		e2qj4B1	A: HTH	X: HTH	H: tetra-helical, lambda repressor-like	T: PK_Tyr_Ser-Thr	F:	ECOD (20:10:01)
A		e2qj4A1	A: Profilin-like	X: sensor domains	H: sensor domains	T: Hydrolase	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	3.50.4.10	Alpha Beta	3-Layer(bba) Sandwich	Hepatocyte Growth Factor	Hepatocyte Growth Factor	CATH (4.3.0)
B	2.40.20.10	Mainly Beta	Beta Barrel	Plasminogen Kringle 4	Plasminogen Kringle 4	CATH (4.3.0)
A	3.50.4.10	Alpha Beta	3-Layer(bba) Sandwich	Hepatocyte Growth Factor	Hepatocyte Growth Factor	CATH (4.3.0)
A	2.40.20.10	Mainly Beta	Beta Barrel	Plasminogen Kringle 4	Plasminogen Kringle 4	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF00051	Kringle domain (Kringle)	Kringle domain	Kringle domains have been found in plasminogen, hepatocyte growth factors, prothrombin, and apolipoprotein A. Structure is disulfide-rich, nearly all-beta.	Domain
A, B	PF00024	PAN domain (PAN_1)	PAN domain	The PAN domain [1] contains a conserved core of three disulphide bridges. In some members of the family there is an additional fourth disulphide bridge the links the N and C termini of the domain. The domain is found in diverse proteins, in some the ...	The PAN domain [1] contains a conserved core of three disulphide bridges. In some members of the family there is an additional fourth disulphide bridge the links the N and C termini of the domain. The domain is found in diverse proteins, in some they mediate protein-protein interactions, in others they mediate protein-carbohydrate interactions.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	Hepatocyte growth factor	protein binding binding signaling receptor binding molecular function activator activity molecular function regulator activity signaling receptor regulator activity growth factor activity receptor ligand activity signaling receptor activator activity chemoattractant activity protein-containing complex binding identical protein binding	developmental process multicellular organism development multicellular organismal process hepaticobiliary system development gland development animal organ development anatomical structure development liver development system development myoblast proliferation cell population proliferation cellular process interleukin-6 production regulation of cellular process developmental process multicellular organism development multicellular organismal process hepaticobiliary system development gland development animal organ development anatomical structure development liver development system development myoblast proliferation cell population proliferation cellular process interleukin-6 production regulation of cellular process negative regulation of biological process regulation of interleukin-6 production regulation of cytokine production cytokine production negative regulation of cellular process regulation of multicellular organismal process negative regulation of macromolecule metabolic process regulation of biosynthetic process regulation of biological process negative regulation of metabolic process biological regulation negative regulation of cytokine production regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulation of gene expression negative regulation of interleukin-6 production negative regulation of gene expression biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process regulation of macromolecule biosynthetic process metabolic process macromolecule metabolic process negative regulation of multicellular organismal process regulation of metabolic process 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 cellular response to stimulus extrinsic apoptotic signaling pathway via death domain receptors response to stimulus signaling negative regulation of signaling regulation of signal transduction extrinsic apoptotic signaling pathway negative regulation of cell communication cell communication negative regulation of extrinsic apoptotic signaling pathway negative regulation of apoptotic signaling pathway signal transduction regulation of signaling cell surface receptor signaling pathway negative regulation of response to stimulus negative regulation of extrinsic apoptotic signaling pathway via death domain receptors negative regulation of signal transduction regulation of extrinsic apoptotic signaling pathway apoptotic signaling pathway regulation of response to stimulus regulation of extrinsic apoptotic signaling pathway via death domain receptors regulation of cell communication regulation of apoptotic signaling pathway regulation of hydrogen peroxide-mediated programmed cell death programmed cell death in response to reactive oxygen species cellular response to oxidative stress cellular response to chemical stress negative regulation of hydrogen peroxide-mediated programmed cell death cellular response to reactive oxygen species hydrogen peroxide-mediated programmed cell death cellular response to stress response to stress response to oxygen-containing compound cellular response to oxygen-containing compound response to reactive oxygen species response to oxidative stress cellular response to chemical stimulus response to chemical regulation of defense response regulation of response to external stimulus negative regulation of inflammatory response defense response response to external stimulus regulation of inflammatory response negative regulation of response to external stimulus regulation of response to stress negative regulation of defense response inflammatory response positive regulation of cell communication regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction positive regulation of signal transduction positive regulation of biological process intracellular signal transduction positive regulation of response to stimulus regulation of intracellular signal transduction intracellular signaling cassette positive regulation of cellular process positive regulation of intracellular signal transduction positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction phosphatidylinositol 3-kinase/protein kinase B signal transduction positive regulation of signaling cell surface receptor protein tyrosine kinase signaling pathway hepatocyte growth factor receptor signaling pathway enzyme-linked receptor protein signaling pathway system process regulation of developmental process regulation of myelination regulation of system process regulation of nervous system development positive regulation of myelination axon ensheathment ensheathment of neurons positive regulation of nervous system process regulation of multicellular organismal development nervous system process nervous system development regulation of nervous system process myelination positive regulation of multicellular organismal process regulation of cellular component organization apoptotic mitochondrial changes regulation of release of cytochrome c from mitochondria cellular component organization negative regulation of release of cytochrome c from mitochondria cellular component organization or biogenesis mitochondrion organization negative regulation of cellular component organization regulation of organelle organization organelle organization release of cytochrome c from mitochondria negative regulation of organelle organization regulation of mitochondrion organization positive regulation of MAPK cascade regulation of MAPK cascade MAPK cascade mesenchymal-epithelial cell signaling branching involved in salivary gland morphogenesis gland morphogenesis salivary gland morphogenesis regulation of branching involved in salivary gland morphogenesis regulation of morphogenesis of an epithelium animal organ morphogenesis regulation of anatomical structure morphogenesis regulation of morphogenesis of a branching structure epithelium development regulation of animal organ morphogenesis morphogenesis of an epithelium salivary gland development cell-cell signaling tissue development regulation of branching involved in salivary gland morphogenesis by mesenchymal-epithelial signaling tissue morphogenesis anatomical structure morphogenesis morphogenesis of a branching structure exocrine system development morphogenesis of a branching epithelium cell chemotaxis chemotaxis taxis cell migration cell motility locomotion cell morphogenesis epithelial cell proliferation regulation of neuron projection development positive regulation of cellular component organization cellular developmental process cell projection organization positive regulation of neuron projection regeneration regulation of cellular response to stress cell development neuron projection development regeneration neuron projection regeneration positive regulation of developmental process neurogenesis neuron differentiation positive regulation of neuron projection development cell differentiation positive regulation of cell projection organization plasma membrane bounded cell projection organization regulation of cell projection organization generation of neurons neuron development regulation of neuron projection regeneration regulation of plasma membrane bounded cell projection organization p38MAPK cascade regulation of p38MAPK cascade angiogenesis regulation of vasculature development tube morphogenesis blood vessel development blood vessel morphogenesis tube development positive regulation of angiogenesis vasculature development circulatory system development positive regulation of vasculature development regulation of angiogenesis anatomical structure formation involved in morphogenesis 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 interleukin-10 production positive regulation of macromolecule biosynthetic process positive regulation of metabolic process positive regulation of biosynthetic process positive regulation of macromolecule metabolic process regulation of interleukin-10 production positive regulation of interleukin-10 production positive regulation of gene expression positive regulation of cytokine production regulation of DNA biosynthetic process regulation of primary metabolic process nucleobase-containing compound metabolic process nucleic acid biosynthetic process regulation of nucleobase-containing compound metabolic process positive regulation of DNA biosynthetic process primary metabolic process DNA metabolic process nucleobase-containing compound biosynthetic process nucleic acid metabolic process positive regulation of DNA metabolic process DNA biosynthetic process regulation of DNA metabolic process cellular response to endogenous stimulus response to hepatocyte growth factor cellular response to growth factor stimulus cellular response to hepatocyte growth factor stimulus response to endogenous stimulus response to growth factor proteolysis protein metabolic process	cellular anatomical structure extracellular region extracellular space

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR018056	Kringle, conserved site	Conserved Site
A, B	IPR003609	PAN/Apple domain	Domain
A, B	IPR043504	Peptidase_S1_PA_chymotrypsin	Unknown
A, B	IPR013806	Kringle-like fold	Homologous Superfamily
A, B	IPR038178	Kringle superfamily	Homologous Superfamily
A, B	IPR009003	Peptidase S1, PA clan	Homologous Superfamily
A, B	IPR050759	Serine proteases and regulators with kringle domains	Family
A, B	IPR001314	Peptidase S1A, chymotrypsin family	Family
A, B	IPR027284	Hepatocyte growth factor	Family
A, B	IPR024174	Hepatocyte growth factor/Macrophage stimulatory protein	Family
A, B	IPR001254	Serine proteases, trypsin domain	Domain
A, B	IPR000001	Kringle	Domain

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.