4BSK | pdb_00004bsk

Crystal structure of VEGF-C in complex with VEGFR-3 domains D1-2

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)
B [auth C]	SCOP2B Superfamily	Cystine-knot cytokines	8070295	3000846	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)
B [auth C]	Phage_lysozyme	e4bskC1	A: a/b three-layered sandwiches	X: immunoglobulin/albumin-binding domain-like	H: EGF-related	T: Complement control module/SCR domain	F: Phage_lysozyme	ECOD (v294.1)
A	VEGFR-1-like_Ig-like	e4bskA3	A: a/b three-layered sandwiches	X: Fusion glycoprotein F2	H: MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase	T: MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase	F: VEGFR-1-like_Ig-like	ECOD (v294.1)
A	C1-set	e4bskA4	A: a/b three-layered sandwiches	X: Fusion glycoprotein F2	H: MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase	T: MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase	F: C1-set	ECOD (v294.1)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B [auth C]	PF00341	PDGF/VEGF domain (PDGF)	PDGF/VEGF domain		Domain
A	PF21339	Vascular endothelial growth factor receptor 1-like, Ig-like domain (VEGFR-1-like_Ig-like)	Vascular endothelial growth factor receptor 1-like, Ig-like domain	This domain is found in Vascular endothelial growth factor receptor 1 from humans (VEGFR-1) and similar proteins from animals. VEGFR-1 is a tyrosine kinase receptor for the placental growth factor (PlGF) that plays an essential role in the developmen ...	This domain is found in Vascular endothelial growth factor receptor 1 from humans (VEGFR-1) and similar proteins from animals. VEGFR-1 is a tyrosine kinase receptor for the placental growth factor (PlGF) that plays an essential role in the development of embryonic vasculature, the regulation of angiogenesis and other essential cellular processes. It consists of seven immunoglobulin-like (Ig-like) domains in its extracellular portion. This entry represents the second of these domains [1-5].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B [auth C]	VASCULAR ENDOTHELIAL GROWTH FACTOR C	molecular function activator activity molecular function regulator activity signaling receptor regulator activity growth factor activity receptor ligand activity signaling receptor activator activity chemoattractant activity protein binding binding signaling receptor binding 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 anatomical structure development animal organ 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 anatomical structure development animal organ 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 cell population proliferation positive regulation of cell population proliferation positive regulation of epithelial cell proliferation regulation of cell population proliferation regulation of epithelial cell proliferation epithelial cell proliferation 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 positive regulation of mesenchymal stem cell proliferation regulation of mesenchymal stem cell proliferation positive regulation of stem cell proliferation stem cell proliferation substrate-dependent cell migration regulation of blood vessel endothelial cell migration endothelial cell migration positive regulation of blood vessel endothelial cell migration positive regulation of endothelial cell migration blood vessel endothelial cell migration regulation of endothelial cell migration regulation of localization establishment of protein localization 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 intracellular protein localization regulation of transport secretion 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 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 process 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 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 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 response to peptide response to cytokine response to leukemia inhibitory factor cellular response to cytokine stimulus cellular response to leukemia inhibitory factor system process circulatory system process regulation of blood pressure regulation of biological quality negative regulation of blood pressure blood circulation	cellular anatomical structure membrane 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 cellular anatomical structure membrane 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
A	VASCULAR ENDOTHELIAL GROWTH FACTOR RECEPTOR 3	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 protein tyrosine kinase activity transmembrane receptor protein tyrosine kinase activity transmembrane receptor protein kinase activity transmembrane signaling receptor activity catalytic activity protein phosphatase 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 protein tyrosine kinase activity transmembrane receptor protein tyrosine kinase activity transmembrane receptor protein kinase activity transmembrane signaling receptor activity catalytic activity protein phosphatase binding phosphatase binding protein binding binding enzyme 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 growth factor binding identical protein binding protein homodimerization activity protein dimerization activity vascular endothelial growth factor receptor activity	cellular response to stimulus regulation of biological process regulation of cellular process cellular response to growth factor stimulus cell surface receptor signaling pathway response to stimulus signaling response to endogenous stimulus biological regulation cell surface receptor protein tyrosine kinase signaling pathway cell communication vascular endothelial growth factor signaling pathway cellular response to endogenous stimulus cellular process cellular response to stimulus regulation of biological process regulation of cellular process cellular response to growth factor stimulus cell surface receptor signaling pathway response to stimulus signaling response to endogenous stimulus biological regulation cell surface receptor protein tyrosine kinase signaling pathway cell communication vascular endothelial growth factor signaling pathway cellular response to endogenous stimulus cellular process cellular response to vascular endothelial growth factor stimulus signal transduction response to growth factor enzyme-linked receptor protein signaling pathway developmental process multicellular organismal process regulation of developmental process regulation of tissue remodeling regulation of blood vessel remodeling anatomical structure morphogenesis blood vessel remodeling tissue remodeling anatomical structure development regulation of multicellular organismal process regulation of anatomical structure morphogenesis blood vessel morphogenesis tube development angiogenesis sprouting angiogenesis vasculature development circulatory system development multicellular organism development tube morphogenesis anatomical structure formation involved in morphogenesis blood vessel development system development cell migration cell motility protein phosphorylation protein autophosphorylation phosphorylation primary metabolic process macromolecule modification phosphate-containing compound metabolic process metabolic process protein metabolic process macromolecule metabolic process protein modification process phosphorus metabolic process positive regulation of cell communication positive regulation of signal transduction positive regulation of biological process regulation of signal transduction intracellular signal transduction positive regulation of response to stimulus positive regulation of JNK cascade regulation of intracellular signal transduction JNK cascade intracellular signaling cassette positive regulation of cellular process regulation of signaling positive regulation of MAPK cascade regulation of JNK cascade positive regulation of intracellular signal transduction regulation of MAPK cascade regulation of response to stimulus MAPK cascade regulation of cell communication positive regulation of signaling positive regulation of locomotion regulation of cell motility endothelial cell migration positive regulation of cell migration regulation of locomotion positive regulation of endothelial cell migration positive regulation of cell motility regulation of cell migration regulation of endothelial cell migration locomotion positive regulation of ERK1 and ERK2 cascade ERK1 and ERK2 cascade regulation of ERK1 and ERK2 cascade positive regulation of macromolecule biosynthetic process positive regulation of metabolic process positive regulation of biosynthetic process regulation of cytokine production cytokine production positive regulation of macromolecule metabolic process regulation of vascular endothelial growth factor production regulation of biosynthetic process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulation of gene expression vascular endothelial growth factor production biosynthetic process positive regulation of gene expression positive regulation of multicellular organismal process positive regulation of vascular endothelial growth factor production regulation of macromolecule biosynthetic process positive regulation of cytokine production regulation of metabolic process negative regulation of programmed cell death regulation of apoptotic process negative regulation of biological process regulation of programmed cell death cell death negative regulation of apoptotic process negative regulation of cellular process apoptotic process programmed cell death lymphangiogenesis lymph vessel morphogenesis lymph vessel development cell population proliferation positive regulation of cell population proliferation regulation of cell population proliferation peptidyl-tyrosine modification peptidyl-amino acid modification peptidyl-tyrosine phosphorylation system process respiratory system process respiratory gaseous exchange by respiratory system positive regulation of phosphorylation regulation of protein modification process regulation of protein phosphorylation positive regulation of protein metabolic process positive regulation of phosphate metabolic process regulation of primary metabolic process positive regulation of protein modification process positive regulation of protein phosphorylation positive regulation of phosphorus metabolic process regulation of protein metabolic process regulation of phosphorus metabolic process regulation of phosphorylation 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 vascular endothelial growth factor receptor signaling pathway animal organ development respiratory tube development lung development respiratory system development lung alveolus development	cellular anatomical structure intracellular anatomical structure cytoplasm protein-containing complex signaling receptor complex cell periphery plasma membrane membrane extracellular region membrane-bounded organelle intracellular organelle organelle nucleus intracellular membrane-bounded organelle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B [auth C]	IPR029034	Cystine-knot cytokine	Homologous Superfamily
B [auth C]	IPR023581	Platelet-derived growth factor, conserved site	Conserved Site
B [auth C]	IPR000072	PDGF/VEGF domain	Domain
B [auth C]	IPR004153	CXCXC repeat	Repeat
B [auth C]	IPR050507	Platelet-derived/Vascular endothelial growth factor	Family
A	IPR001824	Tyrosine-protein kinase, receptor class III, conserved site	Conserved Site
A	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
A	IPR008266	Tyrosine-protein kinase, active site	Active Site
A	IPR020635	Tyrosine-protein kinase, catalytic domain	Domain
A	IPR000719	Protein kinase domain	Domain
A	IPR003599	Immunoglobulin domain subtype	Domain
A	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
A	IPR007110	Immunoglobulin-like domain	Domain
A	IPR055229	VEGFR1-3, fifth immunoglobulin-like domain	Domain
A	IPR055238	VEGFR1-3-like, N-terminal Ig-like domain	Domain
A	IPR017441	Protein kinase, ATP binding site	Binding Site
A	IPR003598	Immunoglobulin subtype 2	Domain
A	IPR001245	Serine-threonine/tyrosine-protein kinase, catalytic domain	Domain
A	IPR013098	Immunoglobulin I-set	Domain
A	IPR011009	Protein kinase-like domain superfamily	Homologous Superfamily
A	IPR041348	VEGFR-2, transmembrane domain	Domain
A	IPR050122	Receptor Tyrosine Kinase	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
B [auth C]	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
A	Pharos: P35916	lymphedema capillary infantile hemangioma polycystic ovary syndrome lymphedema, hereditary, 1A tetralogy of fallot Clear-cell metastatic renal cell carcinoma sarcoma atypical teratoid rhabdoid tumor thyroid gland papillary carcinoma glioblastoma intellectual disability lymphatic system disease malignant mesothelioma non-small cell lung carcinoma thymic carcinoma lymphedema capillary infantile hemangioma polycystic ovary syndrome lymphedema, hereditary, 1A tetralogy of fallot Clear-cell metastatic renal cell carcinoma sarcoma atypical teratoid rhabdoid tumor thyroid gland papillary carcinoma glioblastoma intellectual disability lymphatic system disease malignant mesothelioma non-small cell lung carcinoma thymic carcinoma cancer cerebrovascular disorder endometrial carcinoma hepatocellular carcinoma hydrops fetalis metastatic melanoma osteosarcoma renal cell carcinoma thyroid gland follicular carcinoma gastrointestinal stromal tumor hereditary lymphedema idiopathic pulmonary fibrosis interstitial lung disease