6TJT

Neuropilin2-b1 domain in a complex with the C-terminal VEGFC peptide

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
Protein Modification Annotation

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	8069035	3000087	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	galactose-binding domain-like	8069035	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	PF00754	e6tjtA1	A: beta sandwiches	X: jelly-roll	H: Galactose-binding domain-like (From Topology)	T: Galactose-binding domain-like	F: PF00754	ECOD (1.6)
B	PF00754	e6tjtB1	A: beta sandwiches	X: jelly-roll	H: Galactose-binding domain-like (From Topology)	T: Galactose-binding domain-like	F: PF00754	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	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	Neuropilin-2	cation binding ion binding binding metal ion binding small molecule binding identical protein binding protein binding molecular transducer activity signaling receptor activity transmembrane signaling receptor activity semaphorin receptor activity growth factor binding cytokine binding catalytic activity, acting on a protein cation binding ion binding binding metal ion binding small molecule binding identical protein binding protein binding molecular transducer activity signaling receptor activity transmembrane signaling receptor activity semaphorin receptor activity growth factor binding cytokine binding catalytic activity, acting on a protein kinase activity protein kinase 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 catalytic activity 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 cellular developmental process cell projection organization 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 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 sympathetic neuron projection guidance neuron differentiation neuron projection morphogenesis cell differentiation cellular component organization or biogenesis plasma membrane bounded cell projection organization generation of neurons anatomical structure morphogenesis neuron projection guidance neuron development cellular process blastoderm segmentation segmentation neural crest cell development pattern specification process mesenchyme development embryo development mesenchymal cell migration ameboidal-type cell migration cell migration cell motility neural crest cell migration stem cell development neural crest cell differentiation ventral trunk neural crest cell migration embryonic pattern specification animal organ development regionalization trunk neural crest cell migration stem cell differentiation mesenchymal cell differentiation trunk segmentation axonogenesis motor neuron axon guidance branchiomotor neuron axon guidance axon guidance axon development cell morphogenesis involved in neuron differentiation heart development cardiac chamber morphogenesis heart morphogenesis circulatory system development cardiac septum development cardiac septum morphogenesis cardiac chamber development outflow tract septum morphogenesis outflow tract morphogenesis animal organ morphogenesis 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 neuron migration 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 chemotaxis negative chemotaxis response to stimulus taxis response to chemical response to external stimulus locomotion cell adhesion sensory neuron axon guidance regulation of biological process regulation of cellular component organization regulation of cellular process postsynapse organization biological regulation regulation of postsynapse organization regulation of synapse organization cell junction organization regulation of synapse structure or activity synapse organization regulation of biological quality cranial nerve morphogenesis vestibulocochlear nerve structural organization cranial nerve structural organization vestibulocochlear nerve development vestibulocochlear nerve morphogenesis anatomical structure arrangement parasympathetic nervous system development preganglionic parasympathetic fiber development facial nerve morphogenesis autonomic nervous system development facial nerve structural organization facial nerve development positive regulation of locomotion regulation of cell motility endothelial cell migration positive regulation of biological process positive regulation of cell migration positive regulation of epithelial cell migration tissue migration positive regulation of cell motility regulation of cell migration regulation of endothelial cell migration regulation of multicellular organismal process epithelial cell migration regulation of epithelial cell migration positive regulation of cellular process epithelium migration regulation of locomotion positive regulation of endothelial cell migration blood vessel morphogenesis tube development angiogenesis vasculature development tube morphogenesis anatomical structure formation involved in morphogenesis blood vessel development neural crest cell migration involved in autonomic nervous system development axon extension developmental growth cell growth axon extension involved in axon guidance neuron projection extension involved in neuron projection guidance neuron projection extension developmental cell growth growth developmental growth involved in morphogenesis sympathetic nervous system development sympathetic ganglion development sympathetic neuron projection extension trigeminal nerve development trigeminal nerve structural organization trigeminal nerve morphogenesis cellular response to stimulus cell surface receptor signaling pathway semaphorin-plexin signaling pathway signaling cell communication signal transduction ganglion morphogenesis dorsal root ganglion morphogenesis tissue morphogenesis dorsal root ganglion 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 response to organic substance response to cytokine response to leukemia inhibitory factor cellular response to leukemia inhibitory factor cellular response to chemical stimulus cellular response to cytokine stimulus cellular response to organic substance	cell periphery postsynapse postsynaptic membrane synapse cell junction membrane plasma membrane plasma membrane region cellular anatomical entity synaptic membrane protein-containing complex semaphorin receptor complex receptor complex glutamatergic synapse cell periphery postsynapse postsynaptic membrane synapse cell junction membrane plasma membrane plasma membrane region cellular anatomical entity synaptic membrane protein-containing complex semaphorin receptor complex receptor complex glutamatergic synapse axon cell projection neuron projection plasma membrane bounded cell projection extracellular region
C [auth D], D [auth F]	VEGFC C terminal peptide	protein binding binding molecular function activator activity signaling receptor binding molecular function regulator activity signaling receptor regulator activity growth factor activity receptor ligand activity signaling receptor activator activity chemoattractant activity cytokine receptor binding vascular endothelial growth factor receptor binding growth factor receptor binding vascular endothelial growth factor receptor 3 binding	response to stimulus response to chemical response to xenobiotic stimulus developmental process anatomical structure morphogenesis animal organ development anatomical structure development animal organ morphogenesis positive chemotaxis chemotaxis positive regulation of locomotion regulation of biological process regulation of response to external stimulus positive regulation of positive chemotaxis response to stimulus response to chemical response to xenobiotic stimulus developmental process anatomical structure morphogenesis animal organ development anatomical structure development animal organ morphogenesis positive chemotaxis chemotaxis positive regulation of locomotion regulation of biological process regulation of response to external stimulus positive regulation of positive chemotaxis biological regulation positive regulation of biological process response to external stimulus induction of positive chemotaxis regulation of chemotaxis positive regulation of chemotaxis positive regulation of response to stimulus regulation of positive chemotaxis positive regulation of response to external stimulus taxis regulation of response to stimulus regulation of locomotion locomotion multicellular organismal process regulation of developmental process lymphangiogenesis vasculature development circulatory system development positive regulation of developmental process multicellular organism development regulation of lymphangiogenesis anatomical structure formation involved in morphogenesis positive regulation of lymphangiogenesis lymph vessel morphogenesis lymph vessel development regulation of anatomical structure morphogenesis system development regulation of osteoblast differentiation regulation of cellular process cellular developmental process negative regulation of osteoblast differentiation negative regulation of developmental process negative regulation of biological process regulation of cell differentiation osteoblast differentiation ossification cell differentiation negative regulation of cellular process negative regulation of cell differentiation cellular process cellular response to stimulus cellular response to growth factor stimulus cell surface receptor signaling pathway signaling response to endogenous stimulus cell surface receptor protein tyrosine kinase signaling pathway cell communication vascular endothelial growth factor signaling pathway cellular response to endogenous stimulus cellular response to vascular endothelial growth factor stimulus signal transduction response to growth factor enzyme-linked receptor protein signaling pathway regulation of cell motility positive regulation of cell migration positive regulation of cell motility regulation of cell migration myeloid leukocyte migration cell migration regulation of immune system process cell motility positive regulation of immune system process positive regulation of cellular process regulation of mast cell chemotaxis cell chemotaxis regulation of leukocyte chemotaxis regulation of leukocyte migration mast cell migration positive regulation of leukocyte chemotaxis positive regulation of leukocyte migration leukocyte migration positive regulation of mast cell chemotaxis cellular response to chemical stimulus immune system process mast cell chemotaxis leukocyte chemotaxis blood vessel morphogenesis tube development angiogenesis sprouting angiogenesis tube morphogenesis blood vessel development positive regulation of cell division cell division regulation of cell division morphogenesis of embryonic epithelium epithelium development embryonic morphogenesis morphogenesis of an epithelium tissue development embryo development tissue morphogenesis mesenchymal stem cell proliferation regulation of stem cell proliferation cell population proliferation positive regulation of cell population proliferation positive regulation of mesenchymal stem cell proliferation regulation of mesenchymal stem cell proliferation positive regulation of stem cell proliferation stem cell proliferation regulation of cell population proliferation substrate-dependent cell migration regulation of blood vessel endothelial cell migration endothelial cell migration positive regulation of epithelial cell migration tissue migration ameboidal-type cell migration blood vessel endothelial cell migration regulation of endothelial cell migration epithelial cell migration regulation of multicellular organismal process regulation of epithelial cell migration positive regulation of blood vessel endothelial cell migration epithelium migration positive regulation of endothelial cell migration protein localization regulation of localization establishment of protein localization cellular localization nitrogen compound transport regulation of protein localization transport positive regulation of establishment of protein localization positive regulation of secretion by cell protein localization to extracellular region positive regulation of protein transport localization regulation of secretion by cell secretion by cell positive regulation of secretion cellular macromolecule localization regulation of transport secretion organic substance transport regulation of establishment of protein localization establishment of protein localization to extracellular region export from cell regulation of protein transport protein secretion establishment of localization positive regulation of protein secretion regulation of protein secretion regulation of secretion positive regulation of transport protein transport regulation of cellular localization macromolecule localization positive regulation of protein localization regulation of signal transduction regulation of vascular endothelial growth factor receptor signaling pathway regulation of signaling regulation of cellular response to growth factor stimulus vascular endothelial growth factor receptor signaling pathway regulation of cell communication regulation of vasculature development regulation of multicellular organismal development positive regulation of angiogenesis positive regulation of vasculature development regulation of angiogenesis positive regulation of multicellular organismal process response to decreased oxygen levels response to hypoxia response to stress response to oxygen levels response to abiotic stimulus positive regulation of phosphorylation regulation of protein modification process regulation of protein phosphorylation positive regulation of protein metabolic process positive regulation of cellular metabolic process positive regulation of phosphate metabolic process regulation of primary metabolic process positive regulation of metabolic process positive regulation of protein modification process organic substance metabolic process regulation of phosphate metabolic process phosphate-containing compound metabolic process positive regulation of macromolecule metabolic process protein metabolic process positive regulation of protein phosphorylation phosphorus metabolic process protein modification process organonitrogen compound metabolic process protein phosphorylation positive regulation of phosphorus metabolic process phosphorylation cellular metabolic process regulation of protein metabolic process regulation of cellular metabolic process primary metabolic process regulation of macromolecule metabolic process macromolecule modification regulation of phosphorus metabolic process metabolic process regulation of phosphorylation macromolecule metabolic process regulation of metabolic process positive regulation of nervous system development cell development regulation of neurogenesis regulation of gliogenesis positive regulation of glial cell proliferation positive regulation of gliogenesis regulation of cell development regulation of nervous system development neurogenesis regulation of glial cell proliferation gliogenesis positive regulation of cell differentiation positive regulation of neurogenesis positive regulation of cell development nervous system development glial cell proliferation endothelial cell proliferation positive regulation of epithelial cell proliferation regulation of endothelial cell proliferation positive regulation of endothelial cell proliferation regulation of epithelial cell proliferation epithelial cell proliferation neuroblast proliferation regulation of neuroblast proliferation regulation of neural precursor cell proliferation generation of neurons positive regulation of neural precursor cell proliferation positive regulation of neuroblast proliferation neural precursor cell proliferation protein autophosphorylation regulation of protein autophosphorylation positive regulation of protein autophosphorylation response to organic substance response to cytokine response to leukemia inhibitory factor cellular response to leukemia inhibitory factor cellular response to cytokine stimulus cellular response to organic substance system process circulatory system process regulation of blood pressure regulation of biological quality negative regulation of blood pressure blood circulation	membrane cellular anatomical entity extracellular region membrane-bounded organelle vesicle lumen intracellular anatomical structure intracellular vesicle membrane-enclosed lumen cytoplasmic vesicle lumen intracellular membrane-bounded organelle secretory granule lumen endomembrane system intracellular organelle lumen intracellular organelle membrane cellular anatomical entity extracellular region membrane-bounded organelle vesicle lumen intracellular anatomical structure intracellular vesicle membrane-enclosed lumen cytoplasmic vesicle lumen intracellular membrane-bounded organelle secretory granule lumen endomembrane system intracellular organelle lumen intracellular organelle cytoplasmic vesicle organelle lumen organelle secretory granule secretory vesicle cytoplasm platelet alpha granule vesicle platelet alpha granule lumen extracellular space

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR035914	Spermadhesin, CUB domain superfamily	Homologous Superfamily
A, B	IPR013320	Concanavalin A-like lectin/glucanase domain superfamily	Homologous Superfamily
A, B	IPR000421	Coagulation factor 5/8 C-terminal domain	Domain
A, B	IPR014648	Neuropilin	Family
A, B	IPR008979	Galactose-binding-like domain superfamily	Homologous Superfamily
A, B	IPR000998	MAM domain	Domain
A, B	IPR000859	CUB domain	Domain
A, B	IPR022579	Neuropilin, C-terminal	Domain
C [auth D], D [auth F]	IPR029034	Cystine-knot cytokine	Homologous Superfamily
C [auth D], D [auth F]	IPR023581	Platelet-derived growth factor, conserved site	Conserved Site
C [auth D], D [auth F]	IPR000072	PDGF/VEGF domain	Domain
C [auth D], D [auth F]	IPR004153	CXCXC repeat	Repeat

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B	Pharos: O60462	visual epilepsy tuberculosis interstitial cystitis large cell medulloblastoma malignant colon neoplasm malignant mesothelioma Absence Seizures astrocytic tumor autism ovarian cancer primitive neuroectodermal tumor cystic fibrosis gastric carcinoma glioblastoma invasive ductal breast carcinoma visual epilepsy tuberculosis interstitial cystitis large cell medulloblastoma malignant colon neoplasm malignant mesothelioma Absence Seizures astrocytic tumor autism ovarian cancer primitive neuroectodermal tumor cystic fibrosis gastric carcinoma glioblastoma invasive ductal breast carcinoma lung cancer malignant ependymoma malignant pancreatic neoplasm adenoma oligodendroglioma pancreatic intraductal papillary-mucinous neoplasm lung carcinoma malignant glioma MALT lymphoma adrenal cortex carcinoma atypical teratoid rhabdoid tumor osteosarcoma pilocytic astrocytoma breast cancer subependymal giant cell astrocytoma
C [auth D], D [auth F]	Pharos: P49767	lymphedema, hereditary, 1D melanoma angiosarcoma breast carcinoma breast cancer osteosarcoma pancreatic intraductal papillary-mucinous neoplasm psoriasis adenoma cutaneous melanoma hereditary lymphedema Malignant neoplasm of breast ovarian cancer pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia breast fibroadenoma lymphedema, hereditary, 1D melanoma angiosarcoma breast carcinoma breast cancer osteosarcoma pancreatic intraductal papillary-mucinous neoplasm psoriasis adenoma cutaneous melanoma hereditary lymphedema Malignant neoplasm of breast ovarian cancer pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia breast fibroadenoma cystic fibrosis lymphatic system disease malignant ependymoma pancreatic intraductal papillary-mucinous carcinoma pituitary cancer cancer gastric carcinoma lymphedema malignant mesothelioma

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
C [auth D], D [auth F]	ACE	RESID: AA0041 , AA0042 , AA0043 , AA0044 , AA0045 , AA0046 , AA0049 , AA0050 , AA0051 , AA0052 , AA0053 , AA0054 , AA0354 PSI-MOD : N-acetyl-L-alanine MOD:00050 , N-acetyl-L-aspartic acid MOD:00051 , N-acetyl-L-cysteine MOD:00052 , N-acetyl-S-archeol-cysteine MOD:00897 , N-acetyl-L-glutamic acid MOD:00053 , N-acetyl-L-glutamine MOD:00054 , N-acetylglycine MOD:00055 , N-acetyl-L-methionine MOD:00058 , N-acetyl-L-proline MOD:00059 , N-acetyl-L-serine MOD:00060 , N,O-diacetylated L-serine MOD:00648 , N-acetyl-L-threonine MOD:00061 , N-acetyl-L-tyrosine MOD:00062 , N-acetyl-L-valine MOD:00063 , N2-acetyl-L-arginine MOD:00359

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 R01GM133198.