3P1I | pdb_00003p1i

Ligand binding domain of human ephrin type-B receptor 3

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)
A	d3p1ia1	All beta proteins	Galactose-binding domain-like	Galactose-binding domain-like	Ephrin receptor ligand binding domain	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d3p1ia2	Artifacts	Tags	Tags	Tags	N-terminal Tags	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d3p1ib_	All beta proteins	Galactose-binding domain-like	Galactose-binding domain-like	Ephrin receptor ligand binding domain	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d3p1ic_	All beta proteins	Galactose-binding domain-like	Galactose-binding domain-like	Ephrin receptor ligand binding domain	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)
A	SCOP2 Family	Ephrin receptor ligand binding domain	8082065	4002471	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	galactose-binding domain-like	8082066	3000087	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	galactose-binding domain-like	8082066	3000087	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	galactose-binding domain-like	8082066	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	MoCF_biosynth	e3p1iA1	A: a/b three-layered sandwiches	X: N-terminal beta-sandwich domain in anthrax protective antigen	H: Macro domain-like	T: Macro domain-like	F: MoCF_biosynth	ECOD (v294.1)
B	Gal-bind_lectin	e3p1iB1	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: Gal-bind_lectin	ECOD (v294.1)
C	Gal-bind_lectin	e3p1iC1	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: Gal-bind_lectin	ECOD (v294.1)

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)
B	2.60.120.260	Mainly Beta	Sandwich	Jelly Rolls	Galactose-binding domain-like	CATH (4.3.0)
C	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, B, C	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, B, C	Ephrin type-B receptor 3	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 axon guidance receptor 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	developmental process corpus callosum development multicellular organismal process head development forebrain development animal organ development brain development nervous system development multicellular organism development central nervous system development anatomical structure development telencephalon development system development positive regulation of nervous system development developmental process corpus callosum development multicellular organismal process head development forebrain development animal organ development brain development nervous system development multicellular organism development central nervous system development anatomical structure development telencephalon development system development positive regulation of nervous system development regulation of cellular process positive regulation of cellular component organization regulation of cellular component organization regulation of developmental process positive regulation of biological process regulation of nervous system development positive regulation of developmental process cellular component organization cellular component biogenesis cellular component assembly cell junction assembly regulation of multicellular organismal process regulation of synapse structure or activity synapse organization cellular component organization or biogenesis regulation of synapse assembly regulation of biological quality positive regulation of cellular process regulation of multicellular organismal development regulation of biological process positive regulation of cellular component biogenesis biological regulation regulation of cellular component biogenesis regulation of cell junction assembly positive regulation of cell junction assembly regulation of synapse organization cell junction organization positive regulation of multicellular organismal process cellular process synapse assembly positive regulation of synapse assembly immune system development gland development hematopoietic or lymphoid organ development thymus development immune system process regulation of neuron projection development axonogenesis cellular developmental process cell projection organization plasma membrane bounded cell projection morphogenesis cell development neuron projection development cell morphogenesis neurogenesis cell projection morphogenesis neuron differentiation neuron projection morphogenesis regulation of axonogenesis cell differentiation regulation of anatomical structure morphogenesis plasma membrane bounded cell projection organization regulation of cell projection organization axon development cell morphogenesis involved in neuron differentiation generation of neurons anatomical structure morphogenesis neuron development regulation of plasma membrane bounded cell projection organization blood vessel morphogenesis tube development angiogenesis vasculature development circulatory system development tube morphogenesis anatomical structure formation involved in morphogenesis blood vessel development axon guidance neuron projection guidance retinal ganglion cell axon guidance 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 urogenital system development cell-cell adhesion regulation of cell adhesion regulation of cell-cell adhesion central nervous system neuron development central nervous system neuron differentiation central nervous system projection neuron axonogenesis central nervous system neuron axonogenesis cell migration cell motility dendritic spine development dendrite development dendritic spine morphogenesis dendritic spine organization postsynapse organization dendrite morphogenesis neuron projection organization digestive system development digestive tract development digestive tract morphogenesis neuron recognition neuron projection fasciculation axonal fasciculation cell recognition roof of mouth development	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol cell periphery plasma membrane membrane somatodendritic compartment cell projection dendrite dendritic tree neuron projection plasma membrane bounded cell projection extracellular region

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C	IPR017441	Protein kinase, ATP binding site	Binding Site
A, B, C	IPR001426	Tyrosine-protein kinase, receptor class V, conserved site	Conserved Site
A, B, C	IPR034245	Ephrin type-B receptor 3, ligand binding domain	Domain
A, B, C	IPR008266	Tyrosine-protein kinase, active site	Active Site
A, B, C	IPR001090	Ephrin, ligand binding domain	Domain
A, B, C	IPR008979	Galactose-binding-like domain superfamily	Homologous Superfamily
A, B, C	IPR020635	Tyrosine-protein kinase, catalytic domain	Domain
A, B, C	IPR050449	Ephrin receptor tyrosine kinases	Family
A, B, C	IPR000719	Protein kinase domain	Domain
A, B, C	IPR011641	Tyrosine-protein kinase ephrin type A/B receptor-like	Domain
A, B, C	IPR001245	Serine-threonine/tyrosine-protein kinase, catalytic domain	Domain
A, B, C	IPR013761	Sterile alpha motif/pointed domain superfamily	Homologous Superfamily
A, B, C	IPR003961	Fibronectin type III	Domain
A, B, C	IPR016257	Ephrin receptor type-A /type-B	Family
A, B, C	IPR011009	Protein kinase-like domain superfamily	Homologous Superfamily
A, B, C	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
A, B, C	IPR027936	Ephrin, transmembrane domain	Domain
A, B, C	IPR001660	Sterile alpha motif domain	Domain
A, B, C	IPR036116	Fibronectin type III superfamily	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B, C	Pharos: P54753	Blastic phase chronic myeloid leukemia lung carcinoma non-small cell lung carcinoma psoriasis breast cancer glioblastoma malignant pancreatic neoplasm osteosarcoma lung adenocarcinoma medulloblastoma pancreatic ductal adenocarcinoma primitive neuroectodermal tumor

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.