2XAC

Structural Insights into the Binding of VEGF-B by VEGFR-1D2: Recognition and Specificity

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	d2xaca_	Small proteins	Cystine-knot cytokines	Cystine-knot cytokines	automated matches	automated matches	HUMAN (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d2xacb_	Small proteins	Cystine-knot cytokines	Cystine-knot cytokines	automated matches	automated matches	HUMAN (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d2xacc_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	I set domains	automated matches	HUMAN (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D [auth X]	d2xacx_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	I set domains	automated matches	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	Cystine-knot cytokines	8070297	3000846	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Cystine-knot cytokines	8070297	3000846	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Immunoglobulin (Ig) domain-like	8054805	3000071	SCOP2B (2022-06-29)
D [auth X]	SCOP2B Superfamily	Immunoglobulin (Ig) domain-like	8054805	3000071	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	PDGF	e2xacA1	A: few secondary structure elements	X: Cystine-knot cytokines (From Topology)	H: Cystine-knot cytokines (From Topology)	T: Cystine-knot cytokines	F: PDGF	ECOD (1.6)
B	PDGF	e2xacB1	A: few secondary structure elements	X: Cystine-knot cytokines (From Topology)	H: Cystine-knot cytokines (From Topology)	T: Cystine-knot cytokines	F: PDGF	ECOD (1.6)
C	IG_like	e2xacC1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: IG_like	ECOD (1.6)
D [auth X]	IG_like	e2xacX1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: IG_like	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.10.90.10	Mainly Beta	Ribbon	Cystine Knot Cytokines, subunit B	Cystine-knot cytokines	CATH (4.3.0)
B	2.10.90.10	Mainly Beta	Ribbon	Cystine Knot Cytokines, subunit B	Cystine-knot cytokines	CATH (4.3.0)
C	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
D [auth X]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF00341	PDGF/VEGF domain (PDGF)	PDGF/VEGF domain		Domain
C, D [auth X]	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
A, B	VASCULAR ENDOTHELIAL GROWTH FACTOR B	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 vascular endothelial growth factor receptor 1 binding cytokine receptor binding vascular endothelial growth factor receptor binding growth factor receptor binding chemoattractant activity 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 vascular endothelial growth factor receptor 1 binding cytokine receptor binding vascular endothelial growth factor receptor binding growth factor receptor binding chemoattractant activity heparin binding glycosaminoglycan binding carbohydrate derivative binding sulfur compound binding identical protein 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 cellular response to stimulus positive regulation of cell communication regulation of cellular process positive regulation of signal transduction signaling regulation of signal transduction intracellular signal transduction cell communication positive regulation of ERK1 and ERK2 cascade regulation of intracellular signal transduction intracellular signaling cassette signal transduction positive regulation of cellular process regulation of signaling positive regulation of MAPK cascade positive regulation of intracellular signal transduction regulation of MAPK cascade MAPK cascade regulation of cell communication cellular process ERK1 and ERK2 cascade regulation of ERK1 and ERK2 cascade positive regulation of signaling 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 cellular response to growth factor stimulus cell surface receptor protein tyrosine kinase signaling pathway regulation of vascular endothelial growth factor receptor signaling pathway cellular response to endogenous stimulus enzyme-linked receptor protein signaling pathway cell surface receptor signaling pathway response to endogenous stimulus regulation of cellular response to growth factor stimulus vascular endothelial growth factor receptor signaling pathway positive regulation of vascular endothelial growth factor receptor signaling pathway response to growth factor vascular endothelial growth factor signaling pathway cellular response to vascular endothelial growth factor stimulus 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 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 regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction phosphatidylinositol 3-kinase/protein kinase B signal transduction developmental process multicellular organismal process blood vessel morphogenesis tube development angiogenesis sprouting angiogenesis vasculature development circulatory system development anatomical structure morphogenesis multicellular organism development tube morphogenesis anatomical structure formation involved in morphogenesis anatomical structure development blood vessel development system development neuron apoptotic process negative regulation of neuron apoptotic process regulation of neuron apoptotic process positive regulation of cell division cell division regulation of cell division regulation of developmental process regulation of vasculature development regulation of response to wounding positive regulation of developmental process positive regulation of vascular wound healing vascular wound healing response to stress regulation of response to stress regulation of multicellular organismal process response to wounding regulation of anatomical structure morphogenesis positive regulation of response to wounding wound healing regulation of multicellular organismal development angiogenesis involved in wound healing positive regulation of angiogenesis positive regulation of vasculature development positive regulation of wound healing regulation of angiogenesis regulation of wound healing positive regulation of multicellular organismal process regulation of vascular wound healing cell population proliferation positive regulation of cell population proliferation regulation of cell population proliferation response to decreased oxygen levels response to hypoxia response to oxygen levels response to abiotic stimulus heart process system process circulatory system process cardiac muscle contraction heart contraction muscle contraction muscle system process blood circulation striated muscle contraction regulation of biosynthetic process negative regulation of metabolic process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulation of gene expression negative regulation of gene expression biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process regulation of macromolecule biosynthetic process metabolic process macromolecule metabolic process regulation of metabolic process negative regulation of macromolecule metabolic process 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 heart development animal organ development coronary vasculature development carbohydrate derivative biosynthetic process glycoprotein biosynthetic process carbohydrate derivative metabolic process primary metabolic process glycoprotein metabolic process protein glycosylation glycosylation macromolecule modification macromolecule glycosylation protein O-linked glycosylation protein metabolic process protein modification process regulation of protein modification process positive regulation of phosphorylation regulation of protein phosphorylation positive regulation of protein 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 phosphorus metabolic process positive regulation of protein phosphorylation protein phosphorylation positive regulation of phosphorus metabolic process phosphorylation regulation of protein metabolic process regulation of peptidyl-tyrosine phosphorylation regulation of phosphorylation regulation of phosphorus metabolic process peptidyl-tyrosine phosphorylation	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 extracellular space
C, D [auth X]	VASCULAR ENDOTHELIAL GROWTH FACTOR RECEPTOR 1	molecular transducer activity catalytic activity, acting on a protein ephrin receptor activity kinase activity protein kinase activity signaling receptor activity transferase activity phosphotransferase activity, alcohol group as acceptor transferase activity, transferring phosphorus-containing groups transmembrane-ephrin receptor activity protein tyrosine kinase activity transmembrane receptor protein tyrosine kinase activity transmembrane receptor protein kinase activity transmembrane signaling receptor activity catalytic activity molecular transducer activity catalytic activity, acting on a protein ephrin receptor activity kinase activity protein kinase activity signaling receptor activity transferase activity phosphotransferase activity, alcohol group as acceptor transferase activity, transferring phosphorus-containing groups transmembrane-ephrin receptor activity protein tyrosine kinase activity transmembrane receptor protein tyrosine kinase activity transmembrane receptor protein kinase activity transmembrane signaling receptor activity catalytic activity collagen receptor activity protein tyrosine kinase collagen receptor activity GPI-linked ephrin receptor activity protein-hormone receptor activity insulin receptor activity histone H3Y41 kinase activity histone H3 kinase activity histone modifying activity histone kinase activity placental growth factor receptor activity 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 platelet-derived growth factor beta-receptor activity platelet-derived growth factor receptor activity stem cell factor receptor activity brain-derived neurotrophic factor receptor activity neurotrophin receptor activity insulin-like growth factor receptor activity hepatocyte growth factor receptor activity boss receptor activity epidermal growth factor receptor activity macrophage colony-stimulating factor receptor activity platelet-derived growth factor alpha-receptor activity protein binding growth factor binding fibroblast growth factor receptor activity vascular endothelial growth factor receptor activity histone H2AXY142 kinase activity histone H2AX kinase activity	cellular response to stimulus regulation of biological process regulation of cellular process cell surface receptor signaling pathway response to stimulus signaling biological regulation cell surface receptor protein tyrosine kinase signaling pathway cell communication vascular endothelial growth factor receptor signaling pathway vascular endothelial growth factor receptor-1 signaling pathway cellular process signal transduction enzyme-linked receptor protein signaling pathway cellular response to stimulus regulation of biological process regulation of cellular process cell surface receptor signaling pathway response to stimulus signaling biological regulation cell surface receptor protein tyrosine kinase signaling pathway cell communication vascular endothelial growth factor receptor signaling pathway vascular endothelial growth factor receptor-1 signaling pathway cellular process signal transduction enzyme-linked receptor protein signaling pathway developmental process multicellular organismal process blood vessel morphogenesis tube development angiogenesis sprouting angiogenesis vasculature development circulatory system development anatomical structure morphogenesis multicellular organism development tube morphogenesis anatomical structure formation involved in morphogenesis anatomical structure development blood vessel development system development cell migration cell motility embryonic morphogenesis embryo development 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 negative regulation of cell population proliferation cell population proliferation endothelial cell proliferation negative regulation of biological process regulation of vascular endothelial cell proliferation negative regulation of endothelial cell proliferation negative regulation of vascular endothelial cell proliferation regulation of endothelial cell proliferation regulation of cell population proliferation negative regulation of cellular process regulation of epithelial cell proliferation vascular endothelial cell proliferation epithelial cell proliferation negative regulation of epithelial cell proliferation cellular response to endogenous stimulus cellular response to growth factor stimulus response to endogenous stimulus cellular response to vascular endothelial growth factor stimulus response to growth factor cellular developmental process cell differentiation sensory organ development eye development animal organ development visual system development anatomical structure regression hyaloid vascular plexus regression camera-type eye development sensory system development positive regulation of cell communication regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction positive regulation of signal transduction positive regulation of biological process regulation of signal transduction intracellular signal transduction positive regulation of response to stimulus regulation of intracellular signal transduction intracellular signaling cassette positive regulation of cellular process regulation of signaling positive regulation of intracellular signal transduction positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction regulation of response to stimulus regulation of cell communication phosphatidylinositol 3-kinase/protein kinase B signal transduction positive regulation of signaling positive regulation of cell population proliferation peptidyl-tyrosine modification peptidyl-amino acid modification peptidyl-tyrosine phosphorylation positive regulation of phosphorylation regulation of catalytic activity regulation of transferase activity positive regulation of phosphate metabolic process regulation of MAP kinase activity regulation of primary metabolic process positive regulation of protein serine/threonine kinase activity positive regulation of metabolic process regulation of phosphate metabolic process positive regulation of macromolecule metabolic process positive regulation of protein phosphorylation positive regulation of MAP kinase activity positive regulation of phosphorus metabolic process positive regulation of MAPK cascade regulation of protein metabolic process regulation of MAPK cascade regulation of molecular function positive regulation of kinase activity regulation of kinase activity regulation of protein serine/threonine kinase activity regulation of phosphorus metabolic process regulation of metabolic process regulation of protein modification process regulation of protein phosphorylation positive regulation of protein metabolic process positive regulation of molecular function positive regulation of protein modification process positive regulation of protein kinase activity positive regulation of transferase activity positive regulation of catalytic activity regulation of protein kinase activity regulation of macromolecule metabolic process MAPK cascade regulation of phosphorylation cell chemotaxis chemotaxis response to external stimulus monocyte chemotaxis leukocyte migration cellular response to chemical stimulus taxis immune system process response to chemical mononuclear cell migration myeloid leukocyte migration leukocyte chemotaxis locomotion regulation of developmental process regulation of vasculature development positive regulation of developmental process regulation of multicellular organismal process regulation of anatomical structure morphogenesis regulation of multicellular organismal development positive regulation of angiogenesis positive regulation of vasculature development regulation of angiogenesis positive regulation of multicellular organismal process positive regulation of locomotion regulation of cell motility positive regulation of cell migration regulation of locomotion positive regulation of cell motility regulation of cell migration	intracellular organelle cellular anatomical structure intracellular anatomical structure cytoskeleton organelle membraneless organelle intracellular membraneless organelle actin cytoskeleton protein-containing complex receptor complex extracellular region extracellular space anchoring junction cell junction intracellular organelle cellular anatomical structure intracellular anatomical structure cytoskeleton organelle membraneless organelle intracellular membraneless organelle actin cytoskeleton protein-containing complex receptor complex extracellular region extracellular space anchoring junction cell junction focal adhesion cell-substrate junction cell periphery plasma membrane membrane membrane-bounded organelle endosome intracellular vesicle intracellular membrane-bounded organelle endomembrane system cytoplasmic vesicle cytoplasm vesicle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR029034	Cystine-knot cytokine	Homologous Superfamily
A, B	IPR023581	Platelet-derived growth factor, conserved site	Conserved Site
A, B	IPR000072	PDGF/VEGF domain	Domain
A, B	IPR050507	Platelet-derived/Vascular endothelial growth factor	Family
C, D [auth X]	IPR001824	Tyrosine-protein kinase, receptor class III, conserved site	Conserved Site
C, D [auth X]	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
C, D [auth X]	IPR008266	Tyrosine-protein kinase, active site	Active Site
C, D [auth X]	IPR020635	Tyrosine-protein kinase, catalytic domain	Domain
C, D [auth X]	IPR000719	Protein kinase domain	Domain
C, D [auth X]	IPR013106	Immunoglobulin V-set domain	Domain
C, D [auth X]	IPR003599	Immunoglobulin domain subtype	Domain
C, D [auth X]	IPR013151	Immunoglobulin-like beta-sandwich domain	Domain
C, D [auth X]	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
C, D [auth X]	IPR007110	Immunoglobulin-like domain	Domain
C, D [auth X]	IPR055229	VEGFR1-3, fifth immunoglobulin-like domain	Domain
C, D [auth X]	IPR017441	Protein kinase, ATP binding site	Binding Site
C, D [auth X]	IPR003598	Immunoglobulin subtype 2	Domain
C, D [auth X]	IPR001245	Serine-threonine/tyrosine-protein kinase, catalytic domain	Domain
C, D [auth X]	IPR013098	Immunoglobulin I-set	Domain
C, D [auth X]	IPR011009	Protein kinase-like domain superfamily	Homologous Superfamily
C, D [auth X]	IPR041348	VEGFR-2, transmembrane domain	Domain
C, D [auth X]	IPR050122	Receptor Tyrosine Kinase	Family
C, D [auth X]	IPR009135	Vascular endothelial growth factor receptor 1 (VEGFR1)	Family
C, D [auth X]	IPR055238	VEGFR1-3, N-terminal Ig-like domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B	Pharos: P49765	psoriasis breast carcinoma Mammary Neoplasms, Human pancreatic neoplasm wet macular degeneration alopecia areata breast cancer glioblastoma malignant mesothelioma malignant pancreatic neoplasm attention deficit hyperactivity disorder, inattentive type Crohn disease hypertensive disorder neovascular glaucoma vitiligo psoriasis breast carcinoma Mammary Neoplasms, Human pancreatic neoplasm wet macular degeneration alopecia areata breast cancer glioblastoma malignant mesothelioma malignant pancreatic neoplasm attention deficit hyperactivity disorder, inattentive type Crohn disease hypertensive disorder neovascular glaucoma vitiligo breast fibroadenoma diabetic macular edema ductal breast carcinoma in situ invasive ductal breast carcinoma
C, D [auth X]	Pharos: P17948	renal cell carcinoma melanoma angiosarcoma multiple epiphyseal dysplasia non-small cell lung carcinoma papillary renal cell carcinoma preeclampsia breast carcinoma lung adenocarcinoma skin cancer chromophobe renal cell carcinoma collecting duct carcinoma osteochondrodysplasia interstitial lung disease sarcomatoid renal cell carcinoma renal cell carcinoma melanoma angiosarcoma multiple epiphyseal dysplasia non-small cell lung carcinoma papillary renal cell carcinoma preeclampsia breast carcinoma lung adenocarcinoma skin cancer chromophobe renal cell carcinoma collecting duct carcinoma osteochondrodysplasia interstitial lung disease sarcomatoid renal cell carcinoma skin neoplasm cirrhosis of liver Neoplasm Metastasis uremia breast cancer tuberculosis drug-induced liver injury ovarian cancer heart disease pancreatic intraductal papillary-mucinous neoplasm hepatocellular carcinoma adrenal cortex carcinoma atypical teratoid rhabdoid tumor invasive ductal breast carcinoma malignant glioma spondyloepiphyseal dysplasia tarda, X-linked thyroid gland papillary carcinoma cystic fibrosis myocardial infarction ulcerative colitis gastrointestinal stromal tumor pancreatic ductal adenocarcinoma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia hypertensive disorder pituitary cancer primitive neuroectodermal tumor bladder transitional cell carcinoma kidney disease renal carcinoma cancer lung cancer thymic carcinoma Melnick-Needles syndrome transitional cell carcinoma endometrial carcinoma osteosarcoma glioblastoma pancreatic intraductal papillary-mucinous carcinoma idiopathic pulmonary fibrosis astrocytic tumor intracerebral hemorrhage psoriasis large cell medulloblastoma malignant ependymoma Schwartz-Jampel syndrome malignant pancreatic neoplasm spondyloepiphyseal dysplasia clear cell renal carcinoma medulloblastoma thyroid gland follicular carcinoma cutaneous melanoma