5EX3 | pdb_00005ex3

Crystal structure of human SMYD3 in complex with a VEGFR1 peptide

External Resource: Annotation

Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations
Protein Modification Annotation

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A		e5ex3A1	A: HTH	X: HTH	H: Putative DNA-binding domain	T: Como_SCP	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.170.270.10	Mainly Beta	Beta Complex	Beta-clip-like	SET domain	CATH (4.3.0)
A	6.10.140.2220	Special	Helix non-globular	Helix Hairpins		CATH (4.3.0)
A	1.10.220.160	Mainly Alpha	Orthogonal Bundle	Annexin V	domain 1	CATH (4.3.0)
A	1.25.40.970	Mainly Alpha	Alpha Horseshoe	Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat		CATH (4.3.0)
A	1.25.40.10	Mainly Alpha	Alpha Horseshoe	Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat	Tetratricopeptide repeat domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF00856	SET domain (SET)	SET domain	-	Family
A	PF01753	MYND finger (zf-MYND)	MYND finger		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B [auth D]	VEGFR1 peptide	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 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 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 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 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 cytoplasm cytosol protein-containing complex receptor complex extracellular region extracellular space intracellular organelle cellular anatomical structure intracellular anatomical structure cytoskeleton organelle membraneless organelle intracellular membraneless organelle actin cytoskeleton cytoplasm cytosol 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 vesicle
A	Histone-lysine N-methyltransferase SMYD3	histone H4 methyltransferase activity catalytic activity, acting on a protein transferase activity, transferring one-carbon groups protein methyltransferase activity histone modifying activity transferase activity methyltransferase activity catalytic activity histone methyltransferase activity protein-lysine N-methyltransferase activity histone H3 methyltransferase activity S-adenosylmethionine-dependent methyltransferase activity histone H3K4 methyltransferase activity lysine N-methyltransferase activity histone H4 methyltransferase activity catalytic activity, acting on a protein transferase activity, transferring one-carbon groups protein methyltransferase activity histone modifying activity transferase activity methyltransferase activity catalytic activity histone methyltransferase activity protein-lysine N-methyltransferase activity histone H3 methyltransferase activity S-adenosylmethionine-dependent methyltransferase activity histone H3K4 methyltransferase activity lysine N-methyltransferase activity N-methyltransferase activity histone H3K4 trimethyltransferase activity basal transcription machinery binding RNA polymerase binding protein binding binding RNA polymerase II complex binding basal RNA polymerase II transcription machinery binding RNA polymerase core enzyme binding enzyme binding DNA binding sequence-specific DNA binding double-stranded DNA binding nucleic acid binding RNA polymerase II transcription regulatory region sequence-specific DNA binding cis-regulatory region sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding transcription regulatory region nucleic acid binding RNA polymerase II cis-regulatory region sequence-specific DNA binding histone H3K36 dimethyltransferase activity histone H3K36 methyltransferase activity RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding intronic transcription regulatory region sequence-specific DNA binding cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding	protein-containing complex organization protein-DNA complex assembly cellular component organization protein-DNA complex organization cellular component biogenesis cellular component assembly chromatin organization protein-containing complex assembly chromatin remodeling cellular process cellular component organization or biogenesis nucleosome assembly nucleosome organization localization protein-containing complex organization protein-DNA complex assembly cellular component organization protein-DNA complex organization cellular component biogenesis cellular component assembly chromatin organization protein-containing complex assembly chromatin remodeling cellular process cellular component organization or biogenesis nucleosome assembly nucleosome organization localization establishment of protein localization establishment of localization methylation metabolic process developmental process myotube cell development cellular developmental process cell development muscle cell differentiation myotube differentiation muscle structure development striated muscle cell development muscle cell development cell differentiation anatomical structure development striated muscle cell differentiation regulation of cellular process positive regulation of DNA-templated transcription positive regulation of biological process RNA metabolic process positive regulation of macromolecule biosynthetic process regulation of primary metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process positive regulation of metabolic process DNA-templated transcription regulation of RNA metabolic process transcription by RNA polymerase II positive regulation of biosynthetic process positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process positive regulation of cellular process regulation of RNA biosynthetic process regulation of biosynthetic process regulation of transcription by RNA polymerase II regulation of biological process biological regulation primary metabolic process regulation of macromolecule metabolic process positive regulation of transcription by RNA polymerase II nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process positive regulation of RNA metabolic process regulation of gene expression biosynthetic process positive regulation of RNA biosynthetic process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of DNA-templated transcription regulation of metabolic process cellular response to stimulus response to ketone response to lipid response to stimulus cellular response to endogenous stimulus response to hormone response to steroid hormone cellular response to ketone cellular response to steroid hormone stimulus cellular response to hormone stimulus response to endogenous stimulus cellular response to dexamethasone stimulus response to glucocorticoid cellular response to glucocorticoid stimulus response to oxygen-containing compound cellular response to oxygen-containing compound cellular response to corticosteroid stimulus response to corticosteroid cellular response to chemical stimulus response to chemical cellular response to lipid response to dexamethasone	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B [auth D]	IPR001824	Tyrosine-protein kinase, receptor class III, conserved site	Conserved Site
B [auth D]	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
B [auth D]	IPR008266	Tyrosine-protein kinase, active site	Active Site
B [auth D]	IPR020635	Tyrosine-protein kinase, catalytic domain	Domain
B [auth D]	IPR000719	Protein kinase domain	Domain
B [auth D]	IPR013106	Immunoglobulin V-set domain	Domain
B [auth D]	IPR003599	Immunoglobulin domain subtype	Domain
B [auth D]	IPR013151	Immunoglobulin-like beta-sandwich domain	Domain
B [auth D]	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
B [auth D]	IPR007110	Immunoglobulin-like domain	Domain
B [auth D]	IPR055229	VEGFR1-3, fifth immunoglobulin-like domain	Domain
B [auth D]	IPR055238	VEGFR1-3-like, N-terminal Ig-like domain	Domain
B [auth D]	IPR017441	Protein kinase, ATP binding site	Binding Site
B [auth D]	IPR003598	Immunoglobulin subtype 2	Domain
B [auth D]	IPR001245	Serine-threonine/tyrosine-protein kinase, catalytic domain	Domain
B [auth D]	IPR013098	Immunoglobulin I-set	Domain
B [auth D]	IPR011009	Protein kinase-like domain superfamily	Homologous Superfamily
B [auth D]	IPR041348	VEGFR-2, transmembrane domain	Domain
B [auth D]	IPR050122	Receptor Tyrosine Kinase	Family
B [auth D]	IPR009135	Vascular endothelial growth factor receptor 1 (VEGFR1)	Family
A	IPR002893	Zinc finger, MYND-type	Domain
A	IPR046341	SET domain superfamily	Homologous Superfamily
A	IPR011990	Tetratricopeptide-like helical domain superfamily	Homologous Superfamily
A	IPR001214	SET domain	Domain
A	IPR050869	Histone-lysine N-methyltransferase	Family
A	IPR044420	SMYD3, SET domain	Domain
A	IPR025805	Histone-lysine N-methyltransferase SMYD3	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
B [auth D]	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 uremia Neoplasm Metastasis 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 ulcerative colitis myocardial infarction 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 endometrial carcinoma osteosarcoma 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
A	Pharos: Q9H7B4	amphetamine abuse ductal breast carcinoma in situ malignant mesothelioma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia Amphetamine Addiction invasive ductal breast carcinoma medulloblastoma systemic lupus erythematosus lung cancer ovarian cancer tuberculosis