3MBW | pdb_00003mbw

Crystal structure of the human ephrin A2 LBD and CRD domains in complex with ephrin A1

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
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	d3mbwb_	All beta proteins	Cupredoxin-like	Cupredoxins	automated matches	automated matches	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)
B	SCOP2B Superfamily	Cupredoxins	8061907	3000886	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	galactose-binding domain-like	8082078	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)
B		e3mbwB1	A: Immunoglobulin-like beta-sandwich	X: Immunoglobulin-related	H: Cu,Zn superoxide dismutase-like	T: MR_MLE_C	F:	ECOD (20:10:01)
A		e3mbwA1	A: TIM beta/alpha-barrel	X: TIM barrels	H: TIM barrels	T:	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	2.60.40.420	Mainly Beta	Sandwich	Immunoglobulin-like	Cupredoxins - blue copper proteins	CATH (4.3.0)
A	2.60.120.260	Mainly Beta	Sandwich	Jelly Rolls	Galactose-binding domain-like	CATH (4.3.0)
A	2.60.40.1770	Mainly Beta	Sandwich	Immunoglobulin-like	ephrin a2 ectodomain	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
A	PF25599	Ephrin cysteine rich domain (Ephrin_CRD)	Ephrin cysteine rich domain	This entry represents the cysteine-rich domain found in ephrin proteins. Ephrins are important cell surface proteins that act as ligands for Eph receptor tyrosine kinases	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B	Ephrin-A1	molecular function activator activity molecular function regulator activity signaling receptor regulator activity receptor ligand activity signaling receptor activator activity protein binding binding signaling receptor binding ephrin receptor binding	embryonic organ morphogenesis developmental process multicellular organismal process embryonic morphogenesis animal organ development notochord morphogenesis notochord formation nervous system development embryo development multicellular organism development anatomical structure morphogenesis anatomical structure development anatomical structure formation involved in morphogenesis animal organ morphogenesis embryonic organ morphogenesis developmental process multicellular organismal process embryonic morphogenesis animal organ development notochord morphogenesis notochord formation nervous system development embryo development multicellular organism development anatomical structure morphogenesis anatomical structure development anatomical structure formation involved in morphogenesis animal organ morphogenesis embryonic organ development notochord development system development regulation of multicellular organismal development regulation of biological process regulation of developmental process blood vessel morphogenesis tube development biological regulation angiogenesis vasculature development regulation of vasculature development circulatory system development tube morphogenesis regulation of angiogenesis regulation of multicellular organismal process regulation of anatomical structure morphogenesis blood vessel development amyloid precursor protein catabolic process regulation of cellular process positive regulation of protein metabolic process regulation of protein metabolic process positive regulation of biological process primary metabolic process regulation of amyloid precursor protein catabolic process regulation of macromolecule metabolic process regulation of primary metabolic process positive regulation of metabolic process metabolic process cellular process positive regulation of macromolecule metabolic process protein metabolic process macromolecule metabolic process positive regulation of amyloid precursor protein catabolic process amyloid precursor protein metabolic process regulation of metabolic process positive regulation of cellular process regulation of protein stability regulation of biological quality protein stabilization regulation of neuron projection development axonogenesis regulation of cellular component organization cellular developmental process cell projection organization plasma membrane bounded cell projection morphogenesis cell development neuron projection development cell morphogenesis cellular component organization neurogenesis cell projection morphogenesis neuron differentiation neuron projection morphogenesis regulation of axonogenesis cell differentiation cellular component organization or biogenesis plasma membrane bounded cell projection organization regulation of cell projection organization axon development cell morphogenesis involved in neuron differentiation generation of neurons neuron development regulation of plasma membrane bounded cell projection organization cellular response to stimulus cell surface receptor signaling pathway response to stimulus signaling cell surface receptor protein tyrosine kinase signaling pathway cell communication signal transduction enzyme-linked receptor protein signaling pathway ephrin receptor signaling pathway cell adhesion substrate adhesion-dependent cell spreading cell-substrate adhesion negative regulation of cell adhesion mediated by integrin regulation of cell adhesion mediated by integrin regulation of cell adhesion negative regulation of biological process negative regulation of cell adhesion cell adhesion mediated by integrin negative regulation of cellular process central nervous system neuron differentiation central nervous system development heart morphogenesis heart valve development mesenchyme development endocardial cushion to mesenchymal transition involved in heart valve formation cardiac epithelial to mesenchymal transition heart valve formation endocardial cushion to mesenchymal transition heart development tissue development epithelial to mesenchymal transition heart valve morphogenesis mesenchymal cell differentiation aortic valve development semi-lunar valve development aortic valve morphogenesis negative regulation of dendritic spine morphogenesis regulation of synapse structure or activity synapse organization dendritic spine morphogenesis dendritic spine development postsynapse organization dendritic spine organization negative regulation of cellular component organization regulation of postsynapse organization negative regulation of dendritic spine development regulation of dendritic spine development dendrite development negative regulation of cell projection organization negative regulation of developmental process dendrite morphogenesis negative regulation of neuron projection development regulation of synapse organization cell junction organization regulation of dendritic spine morphogenesis neuron projection organization regulation of amyloid-beta formation positive regulation of amyloid-beta formation amyloid-beta metabolic process amyloid-beta formation regulation of cell motility regulation of blood vessel endothelial cell migration endothelial cell migration regulation of locomotion regulation of cell migration regulation of endothelial cell migration blood vessel endothelial cell migration cell migration cell motility locomotion negative regulation of signaling negative regulation of intracellular signal transduction regulation of signal transduction intracellular signal transduction negative regulation of cell communication regulation of intracellular signal transduction intracellular signaling cassette regulation of signaling negative regulation of response to stimulus regulation of MAPK cascade negative regulation of signal transduction regulation of response to stimulus MAPK cascade regulation of cell communication negative regulation of MAPK cascade positive regulation of cell communication positive regulation of signal transduction positive regulation of intracellular signal transduction positive regulation of response to stimulus positive regulation of signaling positive regulation of MAPK cascade axon guidance neuron projection guidance regulation of epithelial to mesenchymal transition regulation of cell differentiation negative regulation of cell differentiation negative regulation of epithelial to mesenchymal transition negative regulation of multicellular organismal process RNA metabolic process negative regulation of RNA biosynthetic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process regulation of RNA metabolic process transcription by RNA polymerase II negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process negative regulation of macromolecule metabolic process regulation of biosynthetic process regulation of transcription by RNA polymerase II negative regulation of DNA-templated transcription negative regulation of transcription by RNA polymerase II negative regulation of metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process regulation of gene expression biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription negative regulation of RNA metabolic process atrioventricular valve development mitral valve morphogenesis mitral valve development atrioventricular valve morphogenesis negative regulation of thymocyte apoptotic process leukocyte apoptotic process regulation of programmed cell death lymphocyte apoptotic process thymocyte apoptotic process negative regulation of leukocyte apoptotic process regulation of T cell apoptotic process regulation of leukocyte apoptotic process regulation of lymphocyte apoptotic process negative regulation of programmed cell death regulation of apoptotic process cell death negative regulation of T cell apoptotic process negative regulation of apoptotic process regulation of thymocyte apoptotic process T cell apoptotic process apoptotic process programmed cell death negative regulation of lymphocyte apoptotic process	cellular anatomical structure anchoring junction cell junction focal adhesion cell-substrate junction cell periphery plasma membrane membrane side of membrane extracellular region
A	Ephrin type-A receptor 2	molecular transducer activity catalytic activity, acting on a protein kinase activity protein kinase activity signaling receptor 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 binding molecular transducer activity catalytic activity, acting on a protein kinase activity protein kinase activity signaling receptor 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 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 ephrin receptor activity cell adhesion molecule binding cadherin binding protein binding virus receptor activity exogenous protein binding growth factor binding molecular function activator activity molecular function regulator activity	developmental process multicellular organismal process regulation of multicellular organismal development regulation of biological process regulation of developmental process blood vessel morphogenesis tube development biological regulation angiogenesis vasculature development regulation of vasculature development circulatory system development anatomical structure morphogenesis multicellular organism development tube morphogenesis developmental process multicellular organismal process regulation of multicellular organismal development regulation of biological process regulation of developmental process blood vessel morphogenesis tube development biological regulation angiogenesis vasculature development regulation of vasculature development circulatory system development anatomical structure morphogenesis multicellular organism development tube morphogenesis regulation of angiogenesis anatomical structure formation involved in morphogenesis anatomical structure development regulation of multicellular organismal process regulation of anatomical structure morphogenesis blood vessel development system development skeletal system development positive regulation of protein localization to plasma membrane regulation of localization cellular localization regulation of cellular process regulation of protein localization positive regulation of biological process localization intracellular protein 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 regulation of protein localization to cell periphery localization within membrane protein localization to membrane regulation of cellular localization macromolecule localization positive regulation of protein localization cellular process regulation of protein localization to plasma membrane cellular response to stimulus cell surface receptor signaling pathway response to stimulus signaling cell surface receptor protein tyrosine kinase signaling pathway cell communication signal transduction enzyme-linked receptor protein signaling pathway ephrin receptor signaling pathway negative regulation of cell adhesion mediated by integrin regulation of cell adhesion mediated by integrin regulation of cell adhesion negative regulation of biological process negative regulation of cell adhesion cell adhesion cell adhesion mediated by integrin negative regulation of cellular process cell migration cell motility cellular developmental process animal organ development cell development notochord cell development embryo development cell differentiation embryonic organ development notochord development notochord cell differentiation negative regulation of chemokine production regulation of cytokine production cytokine production negative regulation of macromolecule metabolic process regulation of biosynthetic process negative regulation of metabolic process negative regulation of cytokine production regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulation of chemokine production regulation of gene expression negative regulation of gene expression biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process chemokine production regulation of macromolecule biosynthetic process metabolic process macromolecule metabolic process negative regulation of multicellular organismal process regulation of metabolic process post-anal tail morphogenesis lymphangiogenesis negative regulation of developmental process regulation of lymphangiogenesis negative regulation of lymphangiogenesis lymph vessel morphogenesis lymph vessel development regulation of cell motility regulation of blood vessel endothelial cell migration endothelial cell migration regulation of locomotion regulation of cell migration regulation of endothelial cell migration blood vessel endothelial cell migration locomotion cell chemotaxis chemotaxis response to external stimulus cellular response to chemical stimulus taxis response to chemical sensory organ development visual system development cell morphogenesis epithelial cell differentiation eye morphogenesis lens morphogenesis in camera-type eye animal organ morphogenesis sensory system development camera-type eye morphogenesis lens fiber cell morphogenesis epithelium development eye development tissue development lens fiber cell development epithelial cell development sensory organ morphogenesis camera-type eye development lens fiber cell differentiation lens development in camera-type eye 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 cell population proliferation blood vessel endothelial cell proliferation involved in sprouting angiogenesis endothelial cell proliferation sprouting angiogenesis epithelial cell proliferation branching involved in mammary gland duct morphogenesis mammary gland morphogenesis mammary gland development branching morphogenesis of an epithelial tube gland development gland morphogenesis epithelial tube morphogenesis morphogenesis of an epithelium mammary gland duct morphogenesis tissue morphogenesis mammary gland epithelium development morphogenesis of a branching structure morphogenesis of a branching epithelium nucleoside phosphate metabolic process ribose phosphate metabolic process cAMP metabolic process cyclic purine nucleotide metabolic process carbohydrate derivative metabolic process primary metabolic process nucleotide metabolic process cyclic nucleotide metabolic process purine-containing compound metabolic process nucleobase-containing compound metabolic process purine nucleotide metabolic process ribonucleotide metabolic process organophosphate metabolic process nucleobase-containing small molecule metabolic process phosphate-containing compound metabolic process small molecule metabolic process purine ribonucleotide metabolic process phosphorus metabolic process tissue remodeling bone remodeling embryonic organ morphogenesis embryonic morphogenesis notochord morphogenesis notochord formation nervous system development ossification osteoblast differentiation epidermal cell differentiation epidermis development skin development keratinocyte differentiation pericyte cell differentiation formation of primary germ layer mesoderm morphogenesis gastrulation axial mesoderm development axial mesoderm formation axial mesoderm morphogenesis mesoderm formation mesoderm development generation of neurons central nervous system neuron differentiation neurogenesis central nervous system development neuron differentiation mammary gland epithelial cell proliferation cell death apoptotic signaling pathway cellular response to stress DNA damage response response to stress intrinsic apoptotic signaling pathway in response to DNA damage apoptotic process intrinsic apoptotic signaling pathway programmed cell death vasculogenesis positive regulation of locomotion positive regulation of cell migration positive regulation of cell motility response to endogenous stimulus response to growth factor myeloid leukocyte differentiation hemopoiesis myeloid cell differentiation osteoclast differentiation leukocyte differentiation activation of GTPase activity positive regulation of molecular function regulation of molecular function positive regulation of hydrolase activity regulation of catalytic activity regulation of hydrolase activity positive regulation of catalytic activity regulation of GTPase activity positive regulation of GTPase activity defense response inflammatory response neural tube development chordate embryonic development embryo development ending in birth or egg hatching lamellipodium assembly regulation of cellular component organization plasma membrane bounded cell projection organization cell projection organization regulation of cell projection organization regulation of cell projection assembly plasma membrane bounded cell projection assembly regulation of cellular component biogenesis cellular component organization cellular component biogenesis regulation of plasma membrane bounded cell projection assembly regulation of lamellipodium assembly cellular component assembly regulation of lamellipodium organization lamellipodium organization cellular component organization or biogenesis regulation of plasma membrane bounded cell projection organization cell projection assembly negative regulation of blood vessel morphogenesis negative regulation of angiogenesis negative regulation of vasculature development bicellular tight junction assembly positive regulation of cellular component organization tight junction organization cell junction assembly cell-cell junction assembly cell-cell junction organization regulation of bicellular tight junction assembly positive regulation of cellular component biogenesis apical junction assembly regulation of cell junction assembly positive regulation of cell junction assembly positive regulation of bicellular tight junction assembly cell junction organization tight junction assembly biological process involved in interspecies interaction between organisms response to other organism defense response to Gram-positive bacterium response to biotic stimulus defense response to bacterium response to bacterium response to external biotic stimulus	cell projection cellular anatomical structure cell leading edge plasma membrane bounded cell projection lamellipodium protein-containing complex receptor complex anchoring junction cell junction focal adhesion cell-substrate junction ruffle plasma membrane membrane cell projection cellular anatomical structure cell leading edge plasma membrane bounded cell projection lamellipodium protein-containing complex receptor complex anchoring junction cell junction focal adhesion cell-substrate junction ruffle plasma membrane membrane leading edge membrane cell periphery ruffle membrane plasma membrane region cell projection membrane cell surface lamellipodium membrane cell-cell junction tight junction

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B	IPR019765	Ephrin, conserved site	Conserved Site
B	IPR008972	Cupredoxin	Homologous Superfamily
B	IPR031328	Ephrin	Family
B	IPR034252	Ephrin-A ectodomain	Domain
B	IPR001799	Ephrin receptor-binding domain	Domain
A	IPR001426	Tyrosine-protein kinase, receptor class V, conserved site	Conserved Site
A	IPR008266	Tyrosine-protein kinase, active site	Active Site
A	IPR001090	Ephrin, ligand binding domain	Domain
A	IPR020635	Tyrosine-protein kinase, catalytic domain	Domain
A	IPR000719	Protein kinase domain	Domain
A	IPR016257	Ephrin receptor type-A /type-B	Family
A	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
A	IPR027936	Ephrin, transmembrane domain	Domain
A	IPR001660	Sterile alpha motif domain	Domain
A	IPR034263	Ephrin type-A receptor 2, ligand binding domain	Domain
A	IPR017441	Protein kinase, ATP binding site	Binding Site
A	IPR008979	Galactose-binding-like domain superfamily	Homologous Superfamily
A	IPR050449	Ephrin receptor tyrosine kinases	Family
A	IPR001245	Serine-threonine/tyrosine-protein kinase, catalytic domain	Domain
A	IPR013761	Sterile alpha motif/pointed domain superfamily	Homologous Superfamily
A	IPR003961	Fibronectin type III	Domain
A	IPR011009	Protein kinase-like domain superfamily	Homologous Superfamily
A	IPR009030	Growth factor receptor cysteine-rich domain superfamily	Homologous Superfamily
A	IPR036116	Fibronectin type III superfamily	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
B	Pharos: P20827	breast carcinoma pilocytic astrocytoma spina bifida adenoma Down syndrome lung carcinoma malignant pancreatic neoplasm non-alcoholic fatty liver disease pancreatic intraductal papillary-mucinous neoplasm pituitary cancer transitional cell carcinoma attention deficit hyperactivity disorder, inattentive type cutaneous lupus erythematosus gastric adenocarcinoma malignant mesothelioma breast carcinoma pilocytic astrocytoma spina bifida adenoma Down syndrome lung carcinoma malignant pancreatic neoplasm non-alcoholic fatty liver disease pancreatic intraductal papillary-mucinous neoplasm pituitary cancer transitional cell carcinoma attention deficit hyperactivity disorder, inattentive type cutaneous lupus erythematosus gastric adenocarcinoma malignant mesothelioma Mammary Neoplasms ovarian cancer pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia psoriasis ulcerative colitis breast cancer dental caries lung cancer pancreatic intraductal papillary-mucinous carcinoma
A	Pharos: P29317	Noonan syndrome cancer Noonan syndrome with multiple lentigines cataract 6 multiple types cataract nasopharyngeal carcinoma Nuclear non-senile cataract pancreatic intraductal papillary-mucinous neoplasm adrenal cortex carcinoma benign neoplasm sarcoidosis squamous cell lung carcinoma malignant pancreatic neoplasm ovarian cancer atopic eczema Noonan syndrome cancer Noonan syndrome with multiple lentigines cataract 6 multiple types cataract nasopharyngeal carcinoma Nuclear non-senile cataract pancreatic intraductal papillary-mucinous neoplasm adrenal cortex carcinoma benign neoplasm sarcoidosis squamous cell lung carcinoma malignant pancreatic neoplasm ovarian cancer atopic eczema sinusitis gastric adenocarcinoma medulloblastoma non-alcoholic fatty liver disease nuclear cataract pancreatic ductal adenocarcinoma atypical teratoid rhabdoid tumor psoriasis breast cancer spina bifida ulcerative colitis lung carcinoma