4BKF | pdb_00004bkf

crystal structure of the human EphA4 ectodomain in complex with human ephrinB3

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
D	SCOP2B Superfamily	Cupredoxins	8061911	3000886	SCOP2B (2022-06-29)
C	SCOP2 Family	Ephrin ectodomain	8061910	4002092	SCOP2 (2022-06-29)
C	SCOP2 Superfamily	Cupredoxins	8061911	3000886	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	galactose-binding domain-like	8082070	3000087	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	galactose-binding domain-like	8082070	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)
D	PEPCK_N	e4bkfD1	A: a/b three-layered sandwiches	X: PBZ domain	H: PBZ domain	T: PBZ domain	F: PEPCK_N	ECOD (v294.1)
C	PEPCK_N	e4bkfC1	A: a/b three-layered sandwiches	X: PBZ domain	H: PBZ domain	T: PBZ domain	F: PEPCK_N	ECOD (v294.1)
B	Ephrin_lbd	e4bkfB1	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: Fibronectin type I module-like	T: Fibronectin type I module	F: Ephrin_lbd	ECOD (v294.1)
B	Nup160	e4bkfB2	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: Fibronectin type I module-like	T: Fibronectin type I module	F: Nup160	ECOD (v294.1)
A	Ephrin_rec_like	e4bkfA1	A: a/b three-layered sandwiches	X: Alpha-beta plaits	H: Pseudouridine synthase	T: Pseudouridine synthase	F: Ephrin_rec_like	ECOD (v294.1)
A	V_ATPase_I	e4bkfA5	A: a/b three-layered sandwiches	X: Alpha-beta plaits	H: Pseudouridine synthase	T: Pseudouridine synthase	F: V_ATPase_I	ECOD (v294.1)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	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, B	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
A, B	PF00041	Fibronectin type III domain (fn3)	Fibronectin type III domain		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C, D	EPHRIN-B3	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 protein binding binding virus receptor activity exogenous protein binding signaling receptor binding ephrin receptor binding	trans-synaptic signaling regulation of biological process regulation of signaling regulation of cellular process trans-synaptic signaling by trans-synaptic complex signaling trans-synaptic signaling, modulating synaptic transmission modulation of chemical synaptic transmission trans-synaptic signaling by trans-synaptic complex, modulating synaptic transmission biological regulation cell-cell signaling cell communication chemical synaptic transmission synaptic signaling regulation of trans-synaptic signaling trans-synaptic signaling regulation of biological process regulation of signaling regulation of cellular process trans-synaptic signaling by trans-synaptic complex signaling trans-synaptic signaling, modulating synaptic transmission modulation of chemical synaptic transmission trans-synaptic signaling by trans-synaptic complex, modulating synaptic transmission biological regulation cell-cell signaling cell communication chemical synaptic transmission synaptic signaling regulation of trans-synaptic signaling anterograde trans-synaptic signaling regulation of cell communication cellular process multicellular organismal process axonogenesis cellular developmental process cell projection organization plasma membrane bounded cell projection morphogenesis cell development neuron projection development cell morphogenesis cellular component organization neurogenesis multicellular organism development cell projection morphogenesis neuron differentiation neuron projection morphogenesis cell differentiation anatomical structure development cellular component organization or biogenesis system development developmental process plasma membrane bounded cell projection organization axon guidance nervous system development axon development cell morphogenesis involved in neuron differentiation generation of neurons anatomical structure morphogenesis neuron projection guidance neuron development cellular response to stimulus cell surface receptor signaling pathway response to stimulus cell surface receptor protein tyrosine kinase signaling pathway signal transduction enzyme-linked receptor protein signaling pathway ephrin receptor signaling pathway neuron recognition axon choice point recognition cell recognition negative regulation of biological process 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 cellular component organization regulation of developmental process regulation of nervous system development negative regulation of neurogenesis regulation of axonogenesis negative regulation of cellular process 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 regulation of leukocyte activation positive regulation of biological process regulation of cell activation positive regulation of leukocyte cell-cell adhesion lymphocyte activation leukocyte cell-cell adhesion leukocyte activation positive regulation of cell-cell adhesion positive regulation of lymphocyte activation positive regulation of cell activation cell adhesion cell-cell adhesion T cell activation positive regulation of leukocyte activation regulation of immune system process regulation of cell-cell adhesion positive regulation of immune system process positive regulation of cellular process positive regulation of T cell activation positive regulation of cell adhesion regulation of cell adhesion cell activation regulation of T cell activation immune system process lymphocyte costimulation regulation of leukocyte cell-cell adhesion positive regulation of multicellular organismal process T cell costimulation regulation of lymphocyte activation adult walking behavior adult locomotory behavior behavior adult behavior locomotory behavior walking behavior	cellular anatomical structure neuron to neuron synapse synapse cell junction hippocampal mossy fiber to CA3 synapse cell periphery plasma membrane membrane presynapse presynaptic membrane plasma membrane region synaptic membrane glutamatergic synapse
A, B	EPHRIN TYPE-A RECEPTOR 4	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 amyloid-beta binding binding peptide binding GPI-linked ephrin receptor 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 binding DH domain binding protein domain specific binding signaling receptor binding ephrin receptor binding protein tyrosine kinase binding kinase binding enzyme binding protein kinase binding identical protein binding PH domain binding	developmental process ear development sensory organ development inner ear development cochlea development animal organ development anatomical structure development negative regulation of long-term synaptic potentiation positive regulation of cell communication regulation of cellular process modulation of chemical synaptic transmission signaling positive regulation of biological process negative regulation of biological process developmental process ear development sensory organ development inner ear development cochlea development animal organ development anatomical structure development negative regulation of long-term synaptic potentiation positive regulation of cell communication regulation of cellular process modulation of chemical synaptic transmission signaling positive regulation of biological process negative regulation of biological process cell communication long-term synaptic potentiation synaptic signaling regulation of biological quality positive regulation of cellular process regulation of synaptic plasticity trans-synaptic signaling regulation of biological process regulation of signaling biological regulation cell-cell signaling positive regulation of synaptic transmission chemical synaptic transmission regulation of trans-synaptic signaling anterograde trans-synaptic signaling regulation of long-term synaptic potentiation regulation of cell communication cellular process positive regulation of signaling adherens junction organization cellular component organization cell junction organization cellular component organization or biogenesis cell-cell junction organization amyloid precursor protein catabolic process positive regulation of protein metabolic process regulation of protein metabolic 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 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 regulation of protein stability protein stabilization positive regulation of cell adhesion regulation of cell adhesion positive regulation of leukocyte cell-cell adhesion positive regulation of leukocyte adhesion to vascular endothelial cell regulation of leukocyte adhesion to vascular endothelial cell positive regulation of leukocyte adhesion to arterial endothelial cell leukocyte cell-cell adhesion positive regulation of cell-cell adhesion regulation of leukocyte adhesion to arterial endothelial cell cell adhesion cell-cell adhesion leukocyte adhesion to vascular endothelial cell leukocyte adhesion to arterial endothelial cell regulation of leukocyte cell-cell adhesion regulation of cell-cell adhesion cellular response to stimulus cell surface receptor signaling pathway response to stimulus cell surface receptor protein tyrosine kinase signaling pathway signal transduction enzyme-linked receptor protein signaling pathway ephrin receptor signaling pathway multicellular organismal process cellular developmental process regulation of developmental process astrocyte differentiation regulation of glial cell differentiation regulation of cell differentiation nervous system development regulation of astrocyte differentiation multicellular organism development neurogenesis central nervous system development gliogenesis glial cell differentiation cell differentiation system development 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 negative regulation of cellular process negative regulation of response to stimulus regulation of MAPK cascade negative regulation of signal transduction negative regulation of ERK1 and ERK2 cascade regulation of response to stimulus MAPK cascade ERK1 and ERK2 cascade regulation of ERK1 and ERK2 cascade negative regulation of MAPK cascade regulation of neuron projection development regulation of cellular component organization cell projection organization cell development neuron projection development neuron differentiation negative regulation of cell projection organization plasma membrane bounded cell projection organization negative regulation of cellular component organization regulation of cell projection organization negative regulation of neuron projection development generation of neurons neuron development regulation of plasma membrane bounded cell projection organization regulation of cellular response to hypoxia cellular response to oxygen levels cellular response to hypoxia regulation of cellular response to stress cellular response to decreased oxygen levels cellular response to stress regulation of response to stress response to stress response to decreased oxygen levels negative regulation of cellular response to hypoxia cellular response to chemical stimulus response to hypoxia response to chemical response to oxygen levels response to abiotic stimulus plasma membrane bounded cell projection morphogenesis cell morphogenesis cell projection morphogenesis neuron projection morphogenesis anatomical structure morphogenesis neuron projection guidance positive regulation of signal transduction positive regulation of response to stimulus positive regulation of JNK cascade JNK cascade positive regulation of MAPK cascade regulation of JNK cascade positive regulation of intracellular signal transduction negative regulation of locomotion regulation of cell motility regulation of locomotion regulation of cell migration negative regulation of cell motility cell migration cell motility negative regulation of cell migration locomotion regulation of epithelial to mesenchymal transition mesenchyme development negative regulation of cell differentiation regulation of multicellular organismal process negative regulation of developmental process tissue development negative regulation of epithelial to mesenchymal transition epithelial to mesenchymal transition mesenchymal cell differentiation negative regulation of multicellular organismal process adult walking behavior adult locomotory behavior behavior adult behavior locomotory behavior walking behavior regulation of molecular function regulation of catalytic activity regulation of hydrolase activity regulation of GTPase activity negative regulation of cell adhesion neuron projection fasciculation protein biosynthetic process post-transcriptional regulation of gene expression negative regulation of translation negative regulation of protein metabolic process negative regulation of macromolecule metabolic process regulation of biosynthetic process negative regulation of metabolic process gene expression translation macromolecule biosynthetic process regulation of gene expression negative regulation of gene expression biosynthetic process negative regulation of biosynthetic process regulation of translation negative regulation of macromolecule biosynthetic process regulation of macromolecule biosynthetic process axonogenesis regulation of axonogenesis regulation of anatomical structure morphogenesis axon development cell morphogenesis involved in neuron differentiation regulation of synapse structure or activity synapse organization dendritic spine morphogenesis dendritic spine development postsynapse organization dendritic spine organization regulation of postsynapse organization dendrite development dendrite morphogenesis regulation of synapse organization regulation of dendritic spine morphogenesis neuron projection organization motor neuron axon guidance axon guidance cellular component disassembly regulation of synapse pruning cell junction disassembly synapse pruning regulation of modification of synaptic structure modification of synaptic structure neuron apoptotic process negative regulation of neuron apoptotic 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 regulation of neuron apoptotic process cell population proliferation positive regulation of cell population proliferation regulation of cell population proliferation regulation of amyloid-beta formation positive regulation of amyloid-beta formation amyloid-beta metabolic process amyloid-beta formation negative regulation of neuron projection regeneration regeneration neuron projection regeneration response to wounding regulation of axon regeneration response to external stimulus negative regulation of response to external stimulus regulation of neuron projection regeneration negative regulation of axon regeneration regulation of response to external stimulus response to axon injury regulation of response to wounding axon regeneration negative regulation of response to wounding positive regulation of locomotion positive regulation of cell migration positive regulation of cell motility glial cell migration neuron recognition axonal fasciculation cell recognition fasciculation of sensory neuron axon central nervous system neuron development central nervous system neuron differentiation central nervous system projection neuron axonogenesis central nervous system neuron axonogenesis corticospinal tract morphogenesis nerve development innervation cellular response to nitrogen compound response to oxygen-containing compound response to nitrogen compound cellular response to amyloid-beta cellular response to oxygen-containing compound response to amyloid-beta positive regulation of nervous system development regulation of neurogenesis regulation of cell morphogenesis regulation of cell development positive regulation of developmental process regulation of dendrite morphogenesis positive regulation of cell projection organization positive regulation of cell development positive regulation of cell morphogenesis regulation of dendrite development positive regulation of multicellular organismal process positive regulation of cellular component organization regulation of nervous system development positive regulation of cell differentiation positive regulation of neurogenesis regulation of multicellular organismal development positive regulation of dendrite morphogenesis fasciculation of motor neuron axon epithelium development kidney epithelium development nephric duct morphogenesis tube development morphogenesis of an epithelium renal system development tissue morphogenesis tube morphogenesis nephric duct development epithelial tube morphogenesis kidney development	postsynaptic specialization membrane postsynaptic specialization synapse membrane plasma membrane postsynaptic density membrane synaptic membrane cell periphery postsynaptic density postsynapse cellular anatomical structure neuron to neuron synapse organelle cell junction postsynaptic specialization membrane postsynaptic specialization synapse membrane plasma membrane postsynaptic density membrane synaptic membrane cell periphery postsynaptic density postsynapse cellular anatomical structure neuron to neuron synapse organelle cell junction postsynaptic membrane asymmetric synapse plasma membrane region somatodendritic compartment cell body perikaryon neuronal cell body presynapse presynaptic membrane cell projection dendrite dendritic tree neuron projection plasma membrane bounded cell projection intracellular anatomical structure cytoplasm glutamatergic synapse cell-cell junction adherens junction anchoring junction neuromuscular junction dendritic shaft neuron spine dendritic spine membrane-bounded organelle mitochondrial membrane mitochondrion organelle outer membrane intracellular membrane-bounded organelle intracellular organelle organelle envelope bounding membrane of organelle mitochondrial envelope mitochondrial outer membrane outer membrane organelle membrane axon actin-based cell projection filopodium growth cone distal axon axonal growth cone site of polarized growth cell surface endosome membrane early endosome endosome intracellular vesicle early endosome membrane endomembrane system cytoplasmic vesicle membrane cytoplasmic vesicle vesicle membrane vesicle Schaffer collateral - CA1 synapse axon terminus neuron projection terminus

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C, D	IPR019765	Ephrin, conserved site	Conserved Site
C, D	IPR008972	Cupredoxin	Homologous Superfamily
C, D	IPR031328	Ephrin	Family
C, D	IPR001799	Ephrin receptor-binding domain	Domain
A, B	IPR001426	Tyrosine-protein kinase, receptor class V, conserved site	Conserved Site
A, B	IPR034270	Ephrin type-A receptor 4, ligand binding domain	Domain
A, B	IPR008266	Tyrosine-protein kinase, active site	Active Site
A, B	IPR001090	Ephrin, ligand binding domain	Domain
A, B	IPR020635	Tyrosine-protein kinase, catalytic domain	Domain
A, B	IPR000719	Protein kinase domain	Domain
A, B	IPR016257	Ephrin receptor type-A /type-B	Family
A, B	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
A, B	IPR027936	Ephrin, transmembrane domain	Domain
A, B	IPR001660	Sterile alpha motif domain	Domain
A, B	IPR017441	Protein kinase, ATP binding site	Binding Site
A, B	IPR008979	Galactose-binding-like domain superfamily	Homologous Superfamily
A, B	IPR050449	Ephrin receptor tyrosine kinases	Family
A, B	IPR001245	Serine-threonine/tyrosine-protein kinase, catalytic domain	Domain
A, B	IPR013761	Sterile alpha motif/pointed domain superfamily	Homologous Superfamily
A, B	IPR003961	Fibronectin type III	Domain
A, B	IPR011009	Protein kinase-like domain superfamily	Homologous Superfamily
A, B	IPR030602	Ephrin type-A receptor 4, SAM domain	Domain
A, B	IPR036116	Fibronectin type III superfamily	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
C, D	Pharos: Q15768	glioblastoma brain glioma cutaneous melanoma invasive ductal breast carcinoma malignant glioma neuroblastoma ovarian cancer triple-negative breast carcinoma breast cancer esophageal squamous cell carcinoma lung carcinoma malignant mesothelioma oligodendroglioma pituitary cancer uterine corpus leiomyoma glioblastoma brain glioma cutaneous melanoma invasive ductal breast carcinoma malignant glioma neuroblastoma ovarian cancer triple-negative breast carcinoma breast cancer esophageal squamous cell carcinoma lung carcinoma malignant mesothelioma oligodendroglioma pituitary cancer uterine corpus leiomyoma cutaneous lupus erythematosus malignant ependymoma melanoma osteosarcoma skin basal cell carcinoma
A, B	Pharos: P54764	metastatic melanoma pancreatic intraductal papillary-mucinous carcinoma Parkinson disease pilocytic astrocytoma amyotrophic lateral sclerosis atypical teratoid rhabdoid tumor Chronic Myelocytic Leukemia Accelerated Phase cystic fibrosis large cell medulloblastoma malignant ependymoma malignant pancreatic neoplasm oligodendroglioma pancreatic intraductal papillary-mucinous neoplasm tuberculosis asthma metastatic melanoma pancreatic intraductal papillary-mucinous carcinoma Parkinson disease pilocytic astrocytoma amyotrophic lateral sclerosis atypical teratoid rhabdoid tumor Chronic Myelocytic Leukemia Accelerated Phase cystic fibrosis large cell medulloblastoma malignant ependymoma malignant pancreatic neoplasm oligodendroglioma pancreatic intraductal papillary-mucinous neoplasm tuberculosis asthma glioblastoma lung cancer malignant glioma medulloblastoma osteosarcoma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia urinary bladder carcinoma astrocytic tumor breast cancer Crohn disease invasive ductal breast carcinoma lung carcinoma malignant mesothelioma