1WQ9 | pdb_00001wq9

Crystal structure of VR-1, a VEGF-F from a snake venom

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Protein Modification Annotation

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
B	d1wq9b_	Small proteins	Cystine-knot cytokines	Cystine-knot cytokines	Platelet-derived growth factor-like	Vascular endothelial growth factor, VEGF	(Daboia russelii russelii ) [TaxId: 31159 ],	SCOPe (2.08)
A	d1wq9a_	Small proteins	Cystine-knot cytokines	Cystine-knot cytokines	Platelet-derived growth factor-like	Vascular endothelial growth factor, VEGF	(Daboia russelii russelii ) [TaxId: 31159 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2B Superfamily	Cystine-knot cytokines	8043681	3000846	SCOP2B (2022-06-29)
A	SCOP2 Family	Platelet-derived growth factor-like	8031303	4003427	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Cystine-knot cytokines	8043681	3000846	SCOP2 (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	zf-C2H2	e1wq9B1	A: a/b three-layered sandwiches	X: EGF-like	H: EGF-related	T: EGF/Laminin	F: zf-C2H2	ECOD (v294.1)
A	zf-C2H2	e1wq9A1	A: a/b three-layered sandwiches	X: EGF-like	H: EGF-related	T: EGF/Laminin	F: zf-C2H2	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	2.10.90.10	Mainly Beta	Ribbon	Cystine Knot Cytokines, subunit B	Cystine-knot cytokines	CATH (4.3.0)
A	2.10.90.10	Mainly Beta	Ribbon	Cystine Knot Cytokines, subunit B	Cystine-knot cytokines	CATH (4.3.0)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B	Vascular endothelial growth factor	molecular function activator activity molecular function regulator activity signaling receptor regulator activity receptor ligand activity chemoattractant activity signaling receptor activator activity growth factor activity toxin activity protein binding binding signaling receptor binding cytokine receptor binding vascular endothelial growth factor receptor binding growth factor receptor binding	positive chemotaxis chemotaxis positive regulation of locomotion regulation of biological process response to stimulus 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 chemotaxis chemotaxis positive regulation of locomotion regulation of biological process response to stimulus 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 response to chemical regulation of locomotion locomotion multicellular organismal process regulation of developmental process angiogenesis regulation of vasculature development positive regulation of developmental process multicellular organism development tube morphogenesis anatomical structure development regulation of multicellular organismal process regulation of anatomical structure morphogenesis blood vessel development system development developmental process regulation of multicellular organismal development blood vessel morphogenesis tube development positive regulation of angiogenesis vasculature development circulatory system development anatomical structure morphogenesis positive regulation of vasculature development regulation of angiogenesis anatomical structure formation involved in morphogenesis 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 cellular response to stimulus regulation of cellular process 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 process 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 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 vascular endothelial growth factor receptor signaling pathway sprouting angiogenesis	cellular anatomical structure membrane
A	Vascular endothelial growth factor	molecular function activator activity molecular function regulator activity signaling receptor regulator activity receptor ligand activity chemoattractant activity signaling receptor activator activity growth factor activity toxin activity protein binding binding signaling receptor binding cytokine receptor binding vascular endothelial growth factor receptor binding growth factor receptor binding	positive chemotaxis chemotaxis positive regulation of locomotion regulation of biological process response to stimulus 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 chemotaxis chemotaxis positive regulation of locomotion regulation of biological process response to stimulus 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 response to chemical regulation of locomotion locomotion multicellular organismal process regulation of developmental process angiogenesis regulation of vasculature development positive regulation of developmental process multicellular organism development tube morphogenesis anatomical structure development regulation of multicellular organismal process regulation of anatomical structure morphogenesis blood vessel development system development developmental process regulation of multicellular organismal development blood vessel morphogenesis tube development positive regulation of angiogenesis vasculature development circulatory system development anatomical structure morphogenesis positive regulation of vasculature development regulation of angiogenesis anatomical structure formation involved in morphogenesis 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 cellular response to stimulus regulation of cellular process 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 process 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 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 vascular endothelial growth factor receptor signaling pathway sprouting angiogenesis	cellular anatomical structure membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B	IPR023581	Platelet-derived growth factor, conserved site	Conserved Site
B	IPR000072	PDGF/VEGF domain	Domain
B	IPR050507	Platelet-derived/Vascular endothelial growth factor	Family
B	IPR029034	Cystine-knot cytokine	Homologous Superfamily
A	IPR023581	Platelet-derived growth factor, conserved site	Conserved Site
A	IPR000072	PDGF/VEGF domain	Domain
A	IPR050507	Platelet-derived/Vascular endothelial growth factor	Family
A	IPR029034	Cystine-knot cytokine	Homologous Superfamily

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
B	PCA	Parent Component: GLN RESID: AA0031 PSI-MOD : 2-pyrrolidone-5-carboxylic acid (Gln) MOD:00040 , 2-pyrrolidone-5-carboxylic acid (Glu) MOD:00420

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.