1NUK

CRYSTAL STRUCTURE OF THE LIGAND-BINDING DOMAIN OF THE EPHB2 RECEPTOR TYROSINE KINASE

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 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)
A	d1nuka_	All beta proteins	Galactose-binding domain-like	Galactose-binding domain-like	Ephrin receptor ligand binding domain	Ligand-binding domain of the ephb2 receptor tyrosine kinase	house mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	galactose-binding domain-like	8039463	3000087	SCOP2B (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	PF01404	e1nukA1	A: beta sandwiches	X: jelly-roll	H: Galactose-binding domain-like (From Topology)	T: Galactose-binding domain-like	F: PF01404	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.60.120.260	Mainly Beta	Sandwich	Jelly Rolls	Galactose-binding domain-like	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF01404	Ephrin receptor ligand binding domain (Ephrin_lbd)	Ephrin receptor ligand binding domain	The Eph receptors, which bind to ephrins Pfam:PF00812 are a large family of receptor tyrosine kinases. This family represents the amino terminal domain which binds the ephrin ligand [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	PROTEIN (TYROSINE-PROTEIN KINASE RECEPTOR EPH)	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 amide binding amyloid-beta binding binding peptide binding 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-containing complex binding protein binding signaling receptor binding axon guidance receptor activity identical protein binding	cellular response to stimulus cell surface receptor signaling pathway via STAT regulation of biological process regulation of signaling regulation of cellular process cell surface receptor signaling pathway response to stimulus signaling biological regulation regulation of signal transduction cell communication regulation of response to stimulus regulation of receptor signaling pathway via JAK-STAT regulation of cell communication cellular response to stimulus cell surface receptor signaling pathway via STAT regulation of biological process regulation of signaling regulation of cellular process cell surface receptor signaling pathway response to stimulus signaling biological regulation regulation of signal transduction cell communication regulation of response to stimulus regulation of receptor signaling pathway via JAK-STAT regulation of cell communication cellular process signal transduction regulation of receptor signaling pathway via STAT cell surface receptor signaling pathway via JAK-STAT positive regulation of protein localization to plasma membrane protein localization regulation of localization cellular localization regulation of protein localization positive regulation of biological process localization cellular macromolecule localization regulation of protein localization to membrane positive regulation of cellular process positive regulation of protein localization to cell periphery protein localization to cell periphery protein localization to plasma membrane positive regulation of protein localization to membrane localization within membrane regulation of protein localization to cell periphery protein localization to membrane regulation of cellular localization macromolecule localization positive regulation of protein localization regulation of protein localization to plasma membrane catabolic process regulation of cellular component organization macroautophagy autophagy autophagosome organization cellular component biogenesis cellular component organization cellular catabolic process cellular component assembly cellular component organization or biogenesis process utilizing autophagic mechanism autophagosome assembly organelle assembly vacuole organization cellular metabolic process regulation of autophagosome assembly regulation of vacuole organization regulation of cellular component biogenesis regulation of organelle organization organelle organization regulation of organelle assembly metabolic process adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains regulation of T-helper 17 type immune response immune response regulation of adaptive immune response adaptive immune response regulation of adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains immune system process regulation of immune response regulation of immune system process T-helper 17 type immune response regulation of protein modification process regulation of protein phosphorylation negative regulation of biological process negative regulation of phosphate metabolic process negative regulation of cellular metabolic process regulation of primary metabolic process organic substance metabolic process regulation of phosphate metabolic process phosphate-containing compound metabolic process negative regulation of protein modification process negative regulation of cellular process protein metabolic process protein modification process phosphorus metabolic process negative regulation of protein metabolic process negative regulation of macromolecule metabolic process organonitrogen compound metabolic process protein phosphorylation phosphorylation regulation of protein metabolic process negative regulation of metabolic process primary metabolic process regulation of cellular metabolic process regulation of macromolecule metabolic process negative regulation of protein phosphorylation macromolecule modification negative regulation of phosphorus metabolic process regulation of phosphorylation regulation of phosphorus metabolic process macromolecule metabolic process negative regulation of phosphorylation regulation of metabolic process multicellular organismal process B cell activation cell activation lymphocyte activation leukocyte activation negative regulation of signaling negative regulation of intracellular signal transduction intracellular signal transduction negative regulation of cell communication regulation of intracellular signal transduction intracellular signaling cassette negative regulation of response to stimulus regulation of MAPK cascade negative regulation of signal transduction negative regulation of ERK1 and ERK2 cascade MAPK cascade ERK1 and ERK2 cascade regulation of ERK1 and ERK2 cascade negative regulation of MAPK cascade regulation of synaptic plasticity trans-synaptic signaling modulation of chemical synaptic transmission cell-cell signaling chemical synaptic transmission positive regulation of synaptic plasticity synaptic signaling regulation of trans-synaptic signaling anterograde trans-synaptic signaling regulation of biological quality axonogenesis cellular developmental process cell projection organization plasma membrane bounded cell projection morphogenesis cell development central nervous system neuron development neuron projection development cell morphogenesis neurogenesis multicellular organism development central nervous system neuron differentiation cell projection morphogenesis neuron differentiation neuron projection morphogenesis cell differentiation anatomical structure development system development developmental process central nervous system projection neuron axonogenesis central nervous system neuron axonogenesis plasma membrane bounded cell projection organization nervous system development axon development cell morphogenesis involved in neuron differentiation generation of neurons anatomical structure morphogenesis central nervous system development neuron development dendrite development dendritic spine morphogenesis synapse organization dendritic spine development dendritic spine organization postsynapse organization dendrite morphogenesis cell junction organization neuron projection organization neuron recognition neuron projection fasciculation axonal fasciculation cell recognition regulation of cell differentiation regulation of neurogenesis regulation of cell development negative regulation of cellular component organization regulation of cell projection organization negative regulation of axonogenesis negative regulation of multicellular organismal process regulation of neuron projection development regulation of developmental process regulation of nervous system development negative regulation of neurogenesis regulation of axonogenesis negative regulation of nervous system development regulation of multicellular organismal process negative regulation of cell differentiation negative regulation of cell projection organization regulation of anatomical structure morphogenesis regulation of multicellular organismal development negative regulation of developmental process negative regulation of neuron projection development negative regulation of cell development regulation of plasma membrane bounded cell projection organization cell junction assembly regulation of synapse structure or activity regulation of synapse assembly regulation of cell junction assembly regulation of synapse organization synapse assembly cell adhesion regulation of cell adhesion negative regulation of cell adhesion corpus callosum development head development forebrain development animal organ development brain development telencephalon development intercellular transport transport establishment of localization vesicle-mediated intercellular transport vesicle-mediated transport positive regulation of nervous system development positive regulation of cellular component organization positive regulation of developmental process positive regulation of cellular component biogenesis positive regulation of cell junction assembly positive regulation of multicellular organismal process positive regulation of synapse assembly positive regulation of cell communication long-term synaptic potentiation positive regulation of long-term synaptic potentiation positive regulation of synaptic transmission regulation of long-term synaptic potentiation positive regulation of signaling ear morphogenesis embryonic organ morphogenesis ear development sensory organ development embryonic morphogenesis embryo development sensory organ morphogenesis inner ear development inner ear morphogenesis animal organ morphogenesis embryonic organ development axon guidance neuron projection guidance retinal ganglion cell axon guidance negative regulation of ion transmembrane transporter activity negative regulation of NMDA glutamate receptor activity regulation of signaling receptor activity negative regulation of monoatomic ion transport monoatomic ion transmembrane transport regulation of transmembrane transporter activity negative regulation of transport regulation of monoatomic ion transmembrane transport negative regulation of transmembrane transport regulation of transporter activity negative regulation of monoatomic ion transmembrane transport monoatomic ion transport regulation of NMDA receptor activity regulation of monoatomic ion transmembrane transporter activity regulation of transport regulation of monoatomic ion transport negative regulation of molecular function negative regulation of transporter activity transmembrane transport regulation of molecular function regulation of transmembrane transport regulation of neurotransmitter receptor activity negative regulation of signaling receptor activity positive regulation of NMDA glutamate receptor activity positive regulation of molecular function positive regulation of monoatomic ion transport positive regulation of transmembrane transport positive regulation of monoatomic ion transmembrane transport positive regulation of signaling receptor activity positive regulation of transport positive regulation of transporter activity positive regulation of ion transmembrane transporter activity 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 cell migration cell motility locomotion filopodium assembly regulation of cell projection assembly regulation of filopodium assembly plasma membrane bounded cell projection assembly regulation of plasma membrane bounded cell projection assembly cell projection assembly regulation of tumor necrosis factor production cellular biosynthetic process positive regulation of cellular metabolic process positive regulation of macromolecule biosynthetic process positive regulation of metabolic process positive regulation of tumor necrosis factor superfamily cytokine production positive regulation of biosynthetic process cytokine production organic substance biosynthetic process regulation of cytokine production positive regulation of macromolecule metabolic process regulation of biosynthetic process tumor necrosis factor superfamily cytokine production positive regulation of tumor necrosis factor production gene expression macromolecule biosynthetic process tumor necrosis factor production regulation of cellular biosynthetic process regulation of gene expression regulation of tumor necrosis factor superfamily cytokine production biosynthetic process positive regulation of gene expression regulation of macromolecule biosynthetic process positive regulation of cytokine production positive regulation of cellular biosynthetic process cellular response to nitrogen compound response to organic substance response to organonitrogen compound response to endogenous stimulus response to oxygen-containing compound response to nitrogen compound cellular response to amyloid-beta cellular response to oxygen-containing compound cellular response to endogenous stimulus cellular response to chemical stimulus cellular response to organonitrogen compound response to chemical cellular response to organic substance response to amyloid-beta hindbrain development hindbrain tangential cell migration cell migration in hindbrain behavior system process learning learning or memory nervous system process cognition cell surface receptor protein tyrosine kinase signaling pathway enzyme-linked receptor protein signaling pathway ephrin receptor signaling pathway regulation of catalytic activity negative regulation of catalytic activity regulation of transferase activity negative regulation of kinase activity negative regulation of transferase activity regulation of kinase activity negative regulation of protein kinase activity regulation of protein kinase activity regulation of neuronal synaptic plasticity regulation of immune effector process immunoglobulin production positive regulation of immune effector process positive regulation of immune system process positive regulation of immunoglobulin production production of molecular mediator of immune response immune effector process regulation of immunoglobulin production positive regulation of production of molecular mediator of immune response regulation of production of molecular mediator of immune response camera-type eye morphogenesis eye development visual system development eye morphogenesis camera-type eye development sensory system development positive regulation of protein localization to cell surface protein localization to cell surface regulation of protein localization to cell surface positive regulation of cell population proliferation positive regulation of B cell proliferation regulation of leukocyte activation regulation of cell activation leukocyte proliferation positive regulation of lymphocyte activation positive regulation of cell activation regulation of B cell proliferation lymphocyte proliferation regulation of B cell activation positive regulation of leukocyte activation positive regulation of mononuclear cell proliferation regulation of lymphocyte proliferation regulation of leukocyte proliferation cell population proliferation positive regulation of lymphocyte proliferation B cell proliferation positive regulation of B cell activation regulation of cell population proliferation mononuclear cell proliferation positive regulation of leukocyte proliferation regulation of mononuclear cell proliferation regulation of lymphocyte activation positive regulation of dendritic spine morphogenesis positive regulation of dendritic spine development regulation of cell morphogenesis regulation of dendrite morphogenesis positive regulation of cell projection organization positive regulation of cell development regulation of postsynapse organization positive regulation of cell morphogenesis regulation of dendrite development regulation of dendritic spine development positive regulation of neuron projection development positive regulation of cell differentiation positive regulation of neurogenesis positive regulation of dendrite morphogenesis regulation of dendritic spine morphogenesis regulation of body fluid levels blood vessel morphogenesis tube development angiogenesis vasculature development circulatory system development tube morphogenesis anatomical structure formation involved in morphogenesis blood vessel development regulation of defense response behavioral fear response defense response regulation of fear response multicellular organismal response to stress regulation of behavioral fear response regulation of behavior behavioral defense response fear response regulation of response to stress response to stress cranial nerve morphogenesis nerve development cranial nerve development optic nerve morphogenesis optic nerve development urogenital system development biological process involved in interspecies interaction between organisms response to lipid response to other organism cellular response to lipopolysaccharide response to external stimulus cellular response to molecule of bacterial origin response to lipopolysaccharide response to biotic stimulus cellular response to biotic stimulus response to bacterium cellular response to lipid response to external biotic stimulus response to molecule of bacterial origin small GTPase-mediated signal transduction regulation of small GTPase mediated signal transduction regulation of Ras protein signal transduction Ras protein signal transduction negative regulation of small GTPase mediated signal transduction negative regulation of Ras protein signal transduction commissural neuron axon guidance peptidyl-tyrosine modification peptidyl-amino acid modification peptidyl-tyrosine phosphorylation trans-synaptic signaling by trans-synaptic complex trans-synaptic signaling, modulating synaptic transmission trans-synaptic signaling by trans-synaptic complex, modulating synaptic transmission neuron projection retraction tight junction organization tight junction assembly cell-cell junction assembly cell-cell junction organization membrane organization postsynaptic membrane assembly postsynapse assembly membrane biogenesis membrane assembly postsynaptic membrane organization regulation of long-term neuronal synaptic plasticity positive regulation of long-term neuronal synaptic plasticity wound healing regulation of response to external stimulus regulation of blood coagulation hemostasis blood coagulation regulation of coagulation regulation of response to wounding regulation of wound healing coagulation response to wounding regulation of hemostasis roof of mouth development regulation of cytokine production involved in inflammatory response negative regulation of cytokine production involved in inflammatory response production of molecular mediator involved in inflammatory response negative regulation of cytokine production cytokine production involved in inflammatory response negative regulation of cellular biosynthetic process negative regulation of gene expression negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process inflammatory response	neuron spine synapse neuron projection cellular anatomical entity dendritic spine plasma membrane bounded cell projection somatodendritic compartment cell projection postsynapse cell junction dendrite dendritic tree cell surface cell periphery neuron spine synapse neuron projection cellular anatomical entity dendritic spine plasma membrane bounded cell projection somatodendritic compartment cell projection postsynapse cell junction dendrite dendritic tree cell surface cell periphery plasma membrane membrane neuron to neuron synapse hippocampal mossy fiber to CA3 synapse postsynaptic membrane plasma membrane region synaptic membrane presynapse presynaptic membrane glutamatergic synapse cell body neuronal cell body axon membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR020635	Tyrosine-protein kinase, catalytic domain	Domain
A	IPR000719	Protein kinase domain	Domain
A	IPR011641	Tyrosine-protein kinase ephrin type A/B receptor-like	Domain
A	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
A	IPR001090	Ephrin receptor ligand binding domain	Domain
A	IPR017441	Protein kinase, ATP binding site	Binding Site
A	IPR008979	Galactose-binding-like domain superfamily	Homologous Superfamily
A	IPR027936	Ephrin receptor, transmembrane domain	Domain
A	IPR001245	Serine-threonine/tyrosine-protein kinase, catalytic domain	Domain
A	IPR013761	Sterile alpha motif/pointed domain superfamily	Homologous Superfamily
A	IPR009030	Growth factor receptor cysteine-rich domain superfamily	Homologous Superfamily
A	IPR001426	Tyrosine-protein kinase, receptor class V, conserved site	Conserved Site
A	IPR008266	Tyrosine-protein kinase, active site	Active Site
A	IPR034238	Ephrin type-B receptor 2, ligand binding domain	Domain
A	IPR016257	Ephrin receptor type-A /type-B	Family
A	IPR001660	Sterile alpha motif domain	Domain
A	IPR003961	Fibronectin type III	Domain
A	IPR011009	Protein kinase-like domain superfamily	Homologous Superfamily
A	IPR036116	Fibronectin type III superfamily	Homologous Superfamily

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.