5J1X

X-ray structure of neuropilin-1 b1 domain complexed with Arg-5 ligand.

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	d5j1xa_	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	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d5j1xb_	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	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d5j1xc1	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	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d5j1xc2	Artifacts	Tags	Tags	Tags	N-terminal Tags	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D	d5j1xd_	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	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	SCOP2B Superfamily	galactose-binding domain-like	8036296	3000087	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	galactose-binding domain-like	8036296	3000087	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	galactose-binding domain-like	8036296	3000087	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	galactose-binding domain-like	8036296	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	F5_F8_type_C	e5j1xA1	A: beta sandwiches	X: jelly-roll	H: Concanavalin A-like	T: Galactose-binding domain-like	F: F5_F8_type_C	ECOD (1.6)
B	F5_F8_type_C	e5j1xB1	A: beta sandwiches	X: jelly-roll	H: Concanavalin A-like	T: Galactose-binding domain-like	F: F5_F8_type_C	ECOD (1.6)
C	F5_F8_type_C	e5j1xC1	A: beta sandwiches	X: jelly-roll	H: Concanavalin A-like	T: Galactose-binding domain-like	F: F5_F8_type_C	ECOD (1.6)
D	F5_F8_type_C	e5j1xD1	A: beta sandwiches	X: jelly-roll	H: Concanavalin A-like	T: Galactose-binding domain-like	F: F5_F8_type_C	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)
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)
D	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, D	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, B, C, D	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 coreceptor 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 cytokine binding vascular endothelial growth factor binding heparin binding glycosaminoglycan binding carbohydrate derivative binding sulfur compound binding	developmental process multicellular organismal process cranial ganglion development nervous system development tissue development ganglion development multicellular organism development nerve development cranial nerve development facioacoustic ganglion development anatomical structure development system development biological process involved in interspecies interaction between organisms symbiont entry into host cell developmental process multicellular organismal process cranial ganglion development nervous system development tissue development ganglion development multicellular organism development nerve development cranial nerve development facioacoustic ganglion development anatomical structure development system development biological process involved in interspecies interaction between organisms symbiont entry into host cell viral process symbiont entry into host viral life cycle biological process involved in interaction with host biological process involved in symbiotic interaction positive regulation of substrate adhesion-dependent cell spreading regulation of biological process regulation of cellular process regulation of cell-substrate adhesion positive regulation of cell adhesion regulation of substrate adhesion-dependent cell spreading regulation of cell adhesion biological regulation positive regulation of biological process cell-substrate adhesion cell adhesion positive regulation of cell-substrate adhesion substrate adhesion-dependent cell spreading cellular process positive regulation of cellular process blood vessel morphogenesis tube development artery development vasculature development circulatory system development anatomical structure morphogenesis tube morphogenesis artery morphogenesis blood vessel development positive regulation of locomotion regulation of cell motility positive regulation of smooth muscle cell migration regulation of smooth muscle cell migration positive regulation of cell migration smooth muscle cell migration muscle cell migration regulation of locomotion positive regulation of cell motility regulation of cell migration cell migration cell motility locomotion regulation of cellular component organization positive regulation of cellular component organization cell-substrate junction assembly positive regulation of cell-substrate junction organization cellular component organization cellular component biogenesis cellular component assembly cell junction assembly regulation of cell-substrate junction organization cellular component organization or biogenesis 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 heart development cardiac chamber morphogenesis heart morphogenesis animal organ development 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 response to stress response to wounding neuron recognition cellular developmental process cell projection organization cell development neuron projection development neuron projection fasciculation neurogenesis neuron differentiation axonal fasciculation cell differentiation cell recognition plasma membrane bounded cell projection organization axon development generation of neurons neuron development negative regulation of signaling negative regulation of biological process 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 negative regulation of cellular process 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 axonogenesis plasma membrane bounded cell projection morphogenesis cell morphogenesis cell projection morphogenesis neuron projection morphogenesis axon guidance cell morphogenesis involved in neuron differentiation neuron projection guidance sensory neuron axon guidance dendrite development dendrite arborization basal dendrite development dendrite morphogenesis basal dendrite arborization neuron projection arborization basal dendrite morphogenesis positive regulation of cell communication positive regulation of signal transduction intracellular signal transduction positive regulation of response to stimulus 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 positive regulation of signaling 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 axon extension positive regulation of nervous system development regulation of growth regulation of cellular component size developmental growth regulation of cell differentiation regulation of neurogenesis positive regulation of chemotaxis regulation of cell development positive regulation of axon extension involved in axon guidance positive regulation of developmental process taxis positive regulation of cell projection organization regulation of biological quality positive regulation of developmental growth neuron projection extension involved in neuron projection guidance chemotaxis regulation of cell projection organization positive regulation of cell development response to external stimulus developmental growth involved in morphogenesis response to chemical positive regulation of multicellular organismal process regulation of neuron projection development regulation of developmental process regulation of response to external stimulus cell growth regulation of axon extension regulation of nervous system development regulation of axon extension involved in axon guidance regulation of extent of cell growth positive regulation of response to external stimulus positive regulation of cell differentiation regulation of axonogenesis positive regulation of neurogenesis regulation of multicellular organismal process axon extension involved in axon guidance positive regulation of axon extension positive regulation of axonogenesis regulation of anatomical structure morphogenesis regulation of cell size neuron projection extension regulation of multicellular organismal development regulation of developmental growth developmental cell growth growth positive regulation of cell growth regulation of chemotaxis regulation of cell growth positive regulation of growth regulation of plasma membrane bounded cell projection organization regulation of anatomical structure size 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 neuron migration motor neuron migration regulation of localization regulation of transport transport regulation of vesicle-mediated transport establishment of localization vesicle-mediated transport localization cranial nerve morphogenesis trigeminal nerve development trigeminal nerve structural organization cranial nerve structural organization anatomical structure arrangement trigeminal nerve morphogenesis 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 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 sensory organ development retina vasculature development in camera-type eye eye development retina development in camera-type eye visual system development retina vasculature morphogenesis in camera-type eye camera-type eye development sensory system development cell population proliferation positive regulation of cell population proliferation endothelial cell proliferation positive regulation of epithelial cell proliferation regulation of endothelial cell proliferation regulation of cell population proliferation positive regulation of endothelial cell proliferation regulation of epithelial cell proliferation epithelial cell proliferation 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 actin filament bundle assembly regulation of actin cytoskeleton organization regulation of supramolecular fiber organization supramolecular fiber organization cytoskeleton organization regulation of protein modification process positive regulation of phosphorylation regulation of protein phosphorylation positive regulation of protein metabolic process positive regulation of cellular metabolic process peptidyl-tyrosine modification positive regulation of phosphate metabolic process regulation of primary metabolic process positive regulation of metabolic process positive regulation of peptidyl-tyrosine phosphorylation positive regulation of protein modification process regulation of phosphate metabolic process peptidyl-amino acid modification phosphate-containing compound metabolic process positive regulation of macromolecule metabolic process protein metabolic process protein modification process phosphorus metabolic process positive regulation of protein phosphorylation protein phosphorylation positive regulation of phosphorus metabolic process phosphorylation cellular metabolic process regulation of protein metabolic process regulation of peptidyl-tyrosine phosphorylation primary metabolic process regulation of cellular metabolic process regulation of macromolecule metabolic process macromolecule modification metabolic process regulation of phosphorylation regulation of phosphorus metabolic process macromolecule metabolic process peptidyl-tyrosine phosphorylation regulation of metabolic process 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 axonogenesis negative regulation of developmental growth negative regulation of multicellular organismal process negative regulation of neurogenesis negative regulation of nervous system development negative regulation of cell differentiation negative regulation of developmental process negative regulation of axon extension negative regulation of cell development negative regulation of growth negative regulation of cellular component organization negative regulation of axon extension involved in axon guidance negative regulation of cell growth negative regulation of response to external stimulus negative regulation of cell projection organization negative regulation of neuron projection development protein localization cellular localization protein localization to endosome protein localization to organelle cellular macromolecule localization macromolecule localization protein localization to early endosome 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 cell-cell signaling positive chemotaxis cell migration involved in sprouting angiogenesis endothelial cell migration sprouting angiogenesis blood vessel endothelial cell migration 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 cell chemotaxis cellular response to chemical stimulus 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 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 endothelial cell fate commitment endothelium development epithelial cell fate commitment endothelial tip cell fate specification epithelial cell differentiation endothelial cell fate specification blood vessel endothelial cell differentiation blood vessel endothelial cell fate commitment endothelial cell differentiation cell fate specification blood vessel endothelial cell fate specification cell fate commitment 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	intracellular anatomical structure cytoplasm cellular anatomical entity cytosol protein-containing complex receptor complex membrane-bounded organelle sorting endosome endosome intracellular vesicle intracellular membrane-bounded organelle endomembrane system intracellular organelle cytoplasmic vesicle intracellular anatomical structure cytoplasm cellular anatomical entity cytosol protein-containing complex receptor complex membrane-bounded organelle sorting endosome endosome intracellular vesicle intracellular membrane-bounded organelle endomembrane system intracellular organelle cytoplasmic vesicle organelle vesicle extracellular region extracellular space anchoring junction cell junction focal adhesion cell-substrate junction cell periphery plasma membrane membrane postsynapse postsynaptic membrane synapse plasma membrane region synaptic membrane mitochondrial membrane mitochondrion organelle envelope mitochondrial envelope organelle membrane semaphorin receptor complex glutamatergic synapse cell projection neuron projection plasma membrane bounded cell projection axon early endosome polymeric cytoskeletal fiber neurofilament intermediate filament cytoskeleton cytoskeleton intracellular non-membrane-bounded organelle intermediate filament supramolecular fiber supramolecular polymer supramolecular complex non-membrane-bounded organelle

InterPro: Protein Family Classification InterPro Database Homepage

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

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B, C, D	Pharos: O14786	endometriosis prostate cancer liver disease osteosarcoma pancreatic intraductal papillary-mucinous neoplasm peripheral nervous system disease primitive neuroectodermal tumor atypical teratoid rhabdoid tumor tetralogy of fallot invasive ductal breast carcinoma lung adenocarcinoma malignant ependymoma Malignant neoplasm of pancreas migraine disorder ovarian cancer endometriosis prostate cancer liver disease osteosarcoma pancreatic intraductal papillary-mucinous neoplasm peripheral nervous system disease primitive neuroectodermal tumor atypical teratoid rhabdoid tumor tetralogy of fallot invasive ductal breast carcinoma lung adenocarcinoma malignant ependymoma Malignant neoplasm of pancreas migraine disorder ovarian cancer pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia peripheral neuropathy cystic fibrosis tuberculosis glioblastoma lung cancer malignant glioma malignant pancreatic neoplasm nasopharyngeal carcinoma pancreatic intraductal papillary-mucinous carcinoma pancreatic neoplasm pilocytic astrocytoma ulcerative colitis hereditary spastic paraplegia lung carcinoma malignant mesothelioma medulloblastoma

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.