3PDN | pdb_00003pdn

Crystal structure of SmyD3 in complex with methyltransferase inhibitor sinefungin

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

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	PHP	e3pdnA4	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: PHP	ECOD (v294.1)

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
A	SET and MYND domain-containing protein 3	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 RNA polymerase binding protein binding binding RNA polymerase II complex 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
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
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

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.