2ORX | pdb_00002orx

Structural Basis for Ligand Binding and Heparin Mediated Activation of Neuropilin

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)
A	d2orxa1	All beta proteins	Galactose-binding domain-like	Galactose-binding domain-like	Discoidin domain (FA58C, coagulation factor 5/8 C-terminal domain)	B1 domain of neuropilin-1	Norway rat (Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	Cystatin	e2orxA1	A: a/b three-layered sandwiches	X: Profilin-like	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Cystatin	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)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF00754	F5/8 type C domain (F5_F8_type_C)	F5/8 type C domain	This domain is also known as the discoidin (DS) domain family [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Neuropilin-1	cation binding ion binding binding metal ion binding small molecule binding protein binding growth factor binding kinase binding enzyme binding protein kinase binding molecular transducer activity catalytic activity, acting on a protein kinase activity protein kinase activity cation binding ion binding binding metal ion binding small molecule binding protein binding growth factor binding kinase binding enzyme binding protein kinase 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 vascular endothelial growth factor receptor activity protein tyrosine kinase activity transmembrane receptor protein tyrosine kinase activity transmembrane receptor protein kinase activity transmembrane signaling receptor activity catalytic activity GTPase regulator activity enzyme regulator activity enzyme activator activity GTPase activator activity molecular function activator activity nucleoside-triphosphatase regulator activity molecular function regulator activity semaphorin receptor activity vascular endothelial growth factor binding heparin binding glycosaminoglycan binding carbohydrate derivative binding sulfur compound binding	developmental process heart development multicellular organism development multicellular organismal process anatomical structure development animal organ development circulatory system development system development cranial ganglion development nervous system development tissue development ganglion development nerve development cranial nerve development developmental process heart development multicellular organism development multicellular organismal process anatomical structure development animal organ development circulatory system development system development cranial ganglion development nervous system development tissue development ganglion development nerve development cranial nerve development facioacoustic ganglion development axon extension regulation of growth regulation of cellular process axonogenesis regulation of cellular component size developmental growth cell projection organization negative regulation of biological process regulation of cell differentiation regulation of neurogenesis neuron projection development regulation of cell development cell projection morphogenesis neuron differentiation negative regulation of growth neuron projection morphogenesis cell differentiation regulation of biological quality regulation of biological process negative regulation of cellular component organization regulation of cell projection organization negative regulation of cell growth developmental growth involved in morphogenesis generation of neurons negative regulation of axonogenesis negative regulation of developmental growth negative regulation of multicellular organismal process regulation of neuron projection development regulation of cellular component organization cellular developmental process regulation of developmental process plasma membrane bounded cell projection morphogenesis cell development cell growth cell morphogenesis regulation of axon extension cellular component organization regulation of nervous system development neurogenesis negative regulation of neurogenesis regulation of extent of cell growth regulation of axonogenesis negative regulation of cellular process negative regulation of nervous system development regulation of multicellular organismal process negative regulation of cell differentiation cellular component organization or biogenesis negative regulation of cell projection organization regulation of anatomical structure morphogenesis regulation of cell size neuron projection extension regulation of multicellular organismal development regulation of developmental growth plasma membrane bounded cell projection organization developmental cell growth negative regulation of developmental process biological regulation growth negative regulation of axon extension axon development regulation of cell growth cell morphogenesis involved in neuron differentiation negative regulation of neuron projection development anatomical structure morphogenesis negative regulation of cell development neuron development cellular process regulation of plasma membrane bounded cell projection organization regulation of anatomical structure size endothelial cell migration cell migration cell motility positive regulation of substrate adhesion-dependent cell spreading regulation of cell-substrate adhesion positive regulation of cell adhesion regulation of substrate adhesion-dependent cell spreading regulation of cell adhesion positive regulation of biological process cell-substrate adhesion cell adhesion positive regulation of cell-substrate adhesion substrate adhesion-dependent cell spreading positive regulation of cellular process blood vessel morphogenesis tube development artery development vasculature development tube morphogenesis artery morphogenesis blood vessel development positive regulation of cellular component organization cell-substrate junction assembly positive regulation of cell-substrate junction organization cellular component biogenesis cellular component assembly cell junction assembly regulation of cell-substrate junction organization focal adhesion assembly positive regulation of focal adhesion assembly positive regulation of cellular component biogenesis positive regulation of cell-matrix adhesion regulation of cellular component biogenesis regulation of cell junction assembly positive regulation of cell junction assembly cell junction organization cell-matrix adhesion regulation of cell-matrix adhesion cell-substrate junction organization regulation of focal adhesion assembly regulation of cell-substrate junction assembly cellular response to stimulus cell surface receptor signaling pathway response to stimulus neuropilin signaling pathway signaling cell communication signal transduction cardiac chamber morphogenesis heart morphogenesis cardiac septum development cardiac septum morphogenesis cardiac chamber development outflow tract septum morphogenesis outflow tract morphogenesis animal organ morphogenesis platelet-derived growth factor receptor signaling pathway cell surface receptor protein tyrosine kinase signaling pathway enzyme-linked receptor protein signaling pathway angiogenesis involved in coronary vascular morphogenesis coronary vasculature development angiogenesis anatomical structure formation involved in morphogenesis coronary vasculature morphogenesis branching morphogenesis of an epithelial tube epithelial tube morphogenesis epithelium development morphogenesis of an epithelium branching involved in blood vessel morphogenesis tissue morphogenesis morphogenesis of a branching structure morphogenesis of a branching epithelium cranial nerve morphogenesis trigeminal nerve development trigeminal nerve morphogenesis response to stress response to wounding neuron recognition neuron projection fasciculation axonal fasciculation cell recognition negative regulation of signaling regulation of signal transduction regulation of programmed cell death extrinsic apoptotic signaling pathway negative regulation of cell communication negative regulation of extrinsic apoptotic signaling pathway negative regulation of apoptotic signaling pathway regulation of signaling negative regulation of response to stimulus negative regulation of programmed cell death regulation of apoptotic process cell death negative regulation of signal transduction regulation of extrinsic apoptotic signaling pathway apoptotic signaling pathway negative regulation of apoptotic process regulation of response to stimulus regulation of cell communication apoptotic process programmed cell death regulation of apoptotic signaling pathway axon guidance neuron projection guidance sensory neuron axon guidance positive regulation of cell communication positive regulation of signal transduction regulation of platelet-derived growth factor receptor signaling pathway positive regulation of response to stimulus positive regulation of platelet-derived growth factor receptor signaling pathway positive regulation of signaling dendrite development dendrite arborization basal dendrite development dendrite morphogenesis basal dendrite arborization neuron projection arborization basal dendrite morphogenesis sensory organ development retina vasculature development in camera-type eye eye development retina development in camera-type eye visual system development camera-type eye development sensory system development intracellular signal transduction positive regulation of ERK1 and ERK2 cascade regulation of intracellular signal transduction intracellular signaling cassette positive regulation of MAPK cascade positive regulation of intracellular signal transduction regulation of MAPK cascade MAPK cascade ERK1 and ERK2 cascade regulation of ERK1 and ERK2 cascade neural crest cell development mesenchyme development mesenchymal cell migration ameboidal-type cell migration autonomic nervous system development neural crest cell migration stem cell development neural crest cell differentiation stem cell differentiation neural crest cell migration involved in autonomic nervous system development mesenchymal cell differentiation retinal ganglion cell axon guidance positive regulation of nervous system development positive regulation of locomotion positive regulation of chemotaxis positive regulation of axon extension involved in axon guidance positive regulation of developmental process taxis positive regulation of cell projection organization positive regulation of developmental growth chemotaxis positive regulation of cell development response to external stimulus response to chemical regulation of locomotion positive regulation of multicellular organismal process regulation of response to external stimulus regulation of axon extension involved in axon guidance positive regulation of response to external stimulus positive regulation of cell differentiation positive regulation of neurogenesis axon extension involved in axon guidance positive regulation of axon extension positive regulation of axonogenesis locomotion positive regulation of cell growth regulation of chemotaxis positive regulation of growth small GTPase-mediated signal transduction regulation of small GTPase mediated signal transduction regulation of Cdc42 protein signal transduction regulation of Rho protein signal transduction Rho protein signal transduction Cdc42 protein signal transduction sympathetic nervous system development sympathetic ganglion development regulation of cell motility positive regulation of smooth muscle cell chemotaxis regulation of smooth muscle cell chemotaxis regulation of smooth muscle cell migration positive regulation of smooth muscle cell migration positive regulation of cell migration muscle cell migration positive regulation of cell motility smooth muscle cell chemotaxis regulation of cell migration cell chemotaxis smooth muscle cell migration cellular response to chemical stimulus neuron migration motor neuron migration trigeminal nerve structural organization cranial nerve structural organization anatomical structure arrangement cellular response to growth factor stimulus regulation of vascular endothelial growth factor receptor signaling pathway cellular response to endogenous stimulus response to endogenous stimulus regulation of cellular response to growth factor stimulus vascular endothelial growth factor receptor signaling pathway response to growth factor vasculogenesis wound healing filopodium assembly regulation of filopodium assembly plasma membrane bounded cell projection assembly positive regulation of filopodium assembly regulation of cell projection assembly regulation of plasma membrane bounded cell projection assembly cell projection assembly positive regulation of plasma membrane bounded cell projection assembly positive regulation of phosphorylation positive regulation of phosphorus metabolic process phosphorylation positive regulation of phosphate metabolic process positive regulation of metabolic process phosphate-containing compound metabolic process metabolic process regulation of phosphorus metabolic process regulation of phosphorylation phosphorus metabolic process regulation of metabolic process retina vasculature morphogenesis in camera-type eye trigeminal ganglion development positive regulation of organelle organization regulation of cytoskeleton organization regulation of actin filament-based process regulation of actin filament bundle assembly positive regulation of actin filament bundle assembly actin filament bundle organization positive regulation of stress fiber assembly actin filament-based process stress fiber assembly regulation of actin filament organization actin cytoskeleton organization actomyosin structure organization positive regulation of cytoskeleton organization actin filament organization positive regulation of supramolecular fiber organization regulation of organelle organization regulation of stress fiber assembly organelle organization contractile actin filament bundle assembly regulation of actomyosin structure organization regulation of actin cytoskeleton organization actin filament bundle assembly regulation of supramolecular fiber organization supramolecular fiber organization cytoskeleton organization renal artery morphogenesis kidney vasculature development renal system development renal system vasculature development kidney vasculature morphogenesis kidney development renal system vasculature morphogenesis negative regulation of locomotion negative regulation of chemotaxis negative regulation of axon extension involved in axon guidance negative regulation of response to external stimulus localization protein localization to endosome protein localization to organelle macromolecule localization protein localization to early endosome intracellular protein localization sympathetic neuron projection guidance blastoderm segmentation segmentation pattern specification process embryo development ventral trunk neural crest cell migration embryonic pattern specification regionalization trunk neural crest cell migration trunk segmentation blood vessel endothelial cell migration positive chemotaxis cell migration involved in sprouting angiogenesis sprouting angiogenesis hepatocyte growth factor receptor signaling pathway postsynapse organization synapse organization motor neuron axon guidance branchiomotor neuron axon guidance gonadotrophin-releasing hormone neuronal migration to the hypothalamus hypothalamus development forebrain development central nervous system neuron development central nervous system neuron differentiation hypothalamus cell differentiation hypothalamus gonadotrophin-releasing hormone neuron development limbic system development head development forebrain generation of neurons hypothalamus gonadotrophin-releasing hormone neuron differentiation brain development diencephalon development forebrain neuron development central nervous system development hypothalamic tangential migration using cell-axon interactions forebrain neuron differentiation hypothalamus cell migration cellular response to vascular endothelial growth factor stimulus regulation of blood vessel endothelial cell migration regulation of endothelial cell migration positive regulation of cell migration involved in sprouting angiogenesis regulation of cell migration involved in sprouting angiogenesis positive regulation of blood vessel endothelial cell migration positive regulation of endothelial cell migration vestibulocochlear nerve structural organization vestibulocochlear nerve development vestibulocochlear nerve morphogenesis parasympathetic nervous system development preganglionic parasympathetic fiber development facial nerve morphogenesis facial nerve structural organization facial nerve development endothelial cell chemotaxis ectodermal placode development otic placode development integrin-mediated signaling pathway sympathetic neuron projection extension VEGF-activated neuropilin signaling pathway vascular endothelial growth factor signaling pathway neuron apoptotic process negative regulation of neuron apoptotic process regulation of neuron apoptotic process substrate-dependent cell migration, cell extension substrate-dependent cell migration commissural neuron axon guidance regulation of vascular associated smooth muscle cell migration vascular associated smooth muscle cell migration positive regulation of vascular associated smooth muscle cell migration coronary artery morphogenesis semaphorin-plexin signaling pathway gland development branching involved in salivary gland morphogenesis salivary gland development dichotomous subdivision of terminal units involved in salivary gland branching gland morphogenesis dichotomous subdivision of an epithelial terminal unit salivary gland morphogenesis exocrine system development regulation of vasculature development positive regulation of angiogenesis positive regulation of vasculature development regulation of angiogenesis ganglion morphogenesis dorsal root ganglion morphogenesis dorsal root ganglion development response to hepatocyte growth factor cellular response to hepatocyte growth factor stimulus innervation axonogenesis involved in innervation	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle sorting endosome endosome intracellular vesicle intracellular membrane-bounded organelle endomembrane system intracellular organelle cytoplasmic vesicle organelle vesicle cellular anatomical structure intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle sorting endosome endosome intracellular vesicle intracellular membrane-bounded organelle endomembrane system intracellular organelle cytoplasmic vesicle organelle vesicle anchoring junction cell junction focal adhesion cell-substrate junction cell surface cell periphery plasma membrane membrane postsynapse postsynaptic membrane synapse plasma membrane region synaptic membrane mitochondrial membrane mitochondrion organelle envelope mitochondrial envelope organelle membrane glutamatergic synapse cell projection neuron projection plasma membrane bounded cell projection somatodendritic compartment cell body neuronal cell body axon growth cone distal axon site of polarized growth early endosome polymeric cytoskeletal fiber neurofilament intracellular membraneless organelle intermediate filament cytoskeleton cytoskeleton membraneless organelle intermediate filament supramolecular fiber supramolecular polymer supramolecular complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR008979	Galactose-binding-like domain superfamily	Homologous Superfamily
A	IPR000859	CUB domain	Domain
A	IPR022579	Neuropilin, C-terminal	Domain
A	IPR000421	Coagulation factor 5/8, C-terminal domain	Domain
A	IPR035914	Spermadhesin, CUB domain superfamily	Homologous Superfamily
A	IPR013320	Concanavalin A-like lectin/glucanase domain superfamily	Homologous Superfamily
A	IPR014648	Neuropilin	Family
A	IPR050633	Neuropilin/Multicopper Oxidase/Coagulation Factor	Family
A	IPR000998	MAM domain	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.