5ABD

CRYSTAL STRUCTURE OF VEGFR-1 DOMAIN 2 IN PRESENCE OF CU

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 [auth E]	d5abde_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	I set domains	Second domain of the Flt-1 receptor	HUMAN (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B [auth I]	d5abdi_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	I set domains	Second domain of the Flt-1 receptor	HUMAN (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C [auth X]	d5abdx_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	I set domains	Second domain of the Flt-1 receptor	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 [auth E]	SCOP2B Superfamily	Immunoglobulin (Ig) domain-like	8054805	3000071	SCOP2B (2022-06-29)
B [auth I]	SCOP2B Superfamily	Immunoglobulin (Ig) domain-like	8054805	3000071	SCOP2B (2022-06-29)
C [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 [auth E]	IG_like	e5abdE1	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)
B [auth I]	IG_like	e5abdI1	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)
C [auth X]	IG_like	e5abdX1	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 [auth E]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
B [auth I]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
C [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 [auth E], B [auth I], C [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 [auth E], B [auth I], C [auth X]	VASCULAR ENDOTHELIAL GROWTH FACTOR RECEPTOR 1	molecular transducer activity catalytic activity, acting on a protein kinase activity protein kinase activity placental growth factor receptor 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 molecular transducer activity catalytic activity, acting on a protein kinase activity protein kinase activity placental growth factor receptor 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 binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding protein binding growth factor binding vascular endothelial growth factor receptor 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 cell migration cell motility developmental process multicellular organism development multicellular organismal process anatomical structure morphogenesis embryonic morphogenesis anatomical structure development 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 vascular endothelial cell proliferation regulation of epithelial cell proliferation epithelial cell proliferation negative regulation of epithelial cell proliferation blood vessel morphogenesis tube development vasculature development circulatory system development tube morphogenesis blood vessel development system development 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 angiogenesis anatomical structure formation involved in morphogenesis 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 [auth E], B [auth I], C [auth X]	IPR001824	Tyrosine-protein kinase, receptor class III, conserved site	Conserved Site
A [auth E], B [auth I], C [auth X]	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
A [auth E], B [auth I], C [auth X]	IPR008266	Tyrosine-protein kinase, active site	Active Site
A [auth E], B [auth I], C [auth X]	IPR020635	Tyrosine-protein kinase, catalytic domain	Domain
A [auth E], B [auth I], C [auth X]	IPR000719	Protein kinase domain	Domain
A [auth E], B [auth I], C [auth X]	IPR013106	Immunoglobulin V-set domain	Domain
A [auth E], B [auth I], C [auth X]	IPR003599	Immunoglobulin domain subtype	Domain
A [auth E], B [auth I], C [auth X]	IPR013151	Immunoglobulin-like beta-sandwich domain	Domain
A [auth E], B [auth I], C [auth X]	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
A [auth E], B [auth I], C [auth X]	IPR007110	Immunoglobulin-like domain	Domain
A [auth E], B [auth I], C [auth X]	IPR017441	Protein kinase, ATP binding site	Binding Site
A [auth E], B [auth I], C [auth X]	IPR003598	Immunoglobulin subtype 2	Domain
A [auth E], B [auth I], C [auth X]	IPR001245	Serine-threonine/tyrosine-protein kinase, catalytic domain	Domain
A [auth E], B [auth I], C [auth X]	IPR013098	Immunoglobulin I-set	Domain
A [auth E], B [auth I], C [auth X]	IPR011009	Protein kinase-like domain superfamily	Homologous Superfamily
A [auth E], B [auth I], C [auth X]	IPR041348	VEGFR-2, transmembrane domain	Domain
A [auth E], B [auth I], C [auth X]	IPR050122	Receptor Tyrosine Kinase	Family
A [auth E], B [auth I], C [auth X]	IPR009135	Vascular endothelial growth factor receptor 1 (VEGFR1)	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A [auth E], B [auth I], C [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 pancreatic intraductal papillary-mucinous neoplasm heart disease adrenal cortex carcinoma hepatocellular 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 pancreatic ductal adenocarcinoma gastrointestinal stromal tumor pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia pituitary cancer hypertensive disorder primitive neuroectodermal tumor bladder transitional cell carcinoma renal carcinoma cancer kidney disease lung cancer thymic carcinoma transitional cell carcinoma Melnick-Needles syndrome osteosarcoma endometrial carcinoma pancreatic intraductal papillary-mucinous carcinoma glioblastoma astrocytic tumor idiopathic pulmonary fibrosis psoriasis intracerebral hemorrhage large cell medulloblastoma Schwartz-Jampel syndrome malignant ependymoma spondyloepiphyseal dysplasia clear cell renal carcinoma malignant pancreatic neoplasm thyroid gland follicular carcinoma cutaneous melanoma 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.