5HQ8

Co-crystal Structure of human SMYD3 with a MEKK2 peptide at 2.13A

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	PF00856	e5hq8A1	A: beta barrels	X: beta-clip	H: SET domain-like (From Topology)	T: SET domain-like	F: PF00856	ECOD (1.6)
A	F_UNCLASSIFIED	e5hq8A2	A: alpha superhelices	X: Repetitive alpha hairpins	H: ARM repeat (From Topology)	T: ARM repeat	F: F_UNCLASSIFIED	ECOD (1.6)
B	PF00856	e5hq8B1	A: beta barrels	X: beta-clip	H: SET domain-like (From Topology)	T: SET domain-like	F: PF00856	ECOD (1.6)
B	F_UNCLASSIFIED	e5hq8B2	A: alpha superhelices	X: Repetitive alpha hairpins	H: ARM repeat (From Topology)	T: ARM repeat	F: F_UNCLASSIFIED	ECOD (1.6)

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)
B	2.170.270.10	Mainly Beta	Beta Complex	Beta-clip-like	SET domain	CATH (4.3.0)
B	6.10.140.2220	Special	Helix non-globular	Helix Hairpins		CATH (4.3.0)
B	1.10.220.160	Mainly Alpha	Orthogonal Bundle	Annexin V	domain 1	CATH (4.3.0)
B	1.25.40.970	Mainly Alpha	Alpha Horseshoe	Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat		CATH (4.3.0)
B	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, B	PF00856	SET domain (SET)	SET domain	-	Family
A, B	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, B	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 organic cyclic compound 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 ion binding metal ion binding small molecule binding	protein-containing complex organization protein-DNA complex assembly protein-DNA complex organization cellular component 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 protein localization protein-containing complex organization protein-DNA complex assembly protein-DNA complex organization cellular component 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 protein localization localization establishment of protein localization cellular localization cellular macromolecule localization macromolecule 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 muscle cell development cell differentiation anatomical structure development striated muscle cell differentiation regulation of cellular process positive regulation of phosphorylation regulation of protein modification process regulation of protein phosphorylation positive regulation of protein metabolic process positive regulation of biological process regulation of peptidyl-serine phosphorylation positive regulation of cellular metabolic process positive regulation of phosphate metabolic process peptidyl-serine modification regulation of primary metabolic process positive regulation of metabolic process positive regulation of protein modification process organic substance metabolic process peptidyl-serine phosphorylation regulation of phosphate metabolic process phosphate-containing compound metabolic process peptidyl-amino acid modification positive regulation of macromolecule metabolic process protein metabolic process positive regulation of protein phosphorylation phosphorus metabolic process protein modification process positive regulation of cellular process regulation of biological process organonitrogen compound metabolic process protein phosphorylation positive regulation of phosphorus metabolic process phosphorylation cellular metabolic process regulation of protein metabolic process biological regulation regulation of cellular metabolic process primary metabolic process regulation of macromolecule metabolic process positive regulation of peptidyl-serine phosphorylation macromolecule modification regulation of phosphorus metabolic process regulation of phosphorylation macromolecule metabolic process regulation of metabolic process positive regulation of macromolecule biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription regulation of RNA metabolic process transcription by RNA polymerase II organic substance biosynthetic process regulation of nucleobase-containing compound metabolic process regulation of transcription by RNA polymerase II positive regulation of nucleobase-containing compound metabolic process positive regulation of transcription by RNA polymerase II positive regulation of RNA metabolic process organic cyclic compound metabolic process regulation of gene expression biosynthetic process organic cyclic compound biosynthetic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription positive regulation of DNA-templated transcription cellular biosynthetic process RNA metabolic process RNA biosynthetic process nucleic acid biosynthetic process positive regulation of biosynthetic process regulation of RNA biosynthetic process regulation of biosynthetic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process regulation of cellular biosynthetic process positive regulation of RNA biosynthetic process positive regulation of cellular biosynthetic process cellular response to stimulus response to organic substance response to ketone response to stimulus response to lipid cellular response to endogenous stimulus response to hormone response to steroid hormone cellular response to organic substance cellular response to ketone cellular response to steroid hormone stimulus response to organic cyclic compound cellular response to hormone stimulus response to endogenous stimulus cellular response to dexamethasone stimulus response to glucocorticoid cellular response to organic cyclic compound 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	intracellular anatomical structure cytoplasm cellular anatomical entity cytosol membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen
C [auth I], D [auth J]	MEKK2 peptide	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 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 kinase binding enzyme binding protein kinase binding catalytic activity, acting on a protein kinase activity protein kinase activity transferase activity catalytic activity phosphotransferase activity, alcohol group as acceptor transferase activity, transferring phosphorus-containing groups protein serine/threonine kinase activity MAP kinase kinase kinase activity cation binding metal ion binding protein serine kinase activity	cellular response to stimulus response to stimulus response to mechanical stimulus response to external stimulus response to abiotic stimulus cellular process cellular response to mechanical stimulus cellular response to abiotic stimulus cellular response to external stimulus cellular response to environmental stimulus phosphorylation cellular metabolic process phosphate-containing compound metabolic process metabolic process cellular response to stimulus response to stimulus response to mechanical stimulus response to external stimulus response to abiotic stimulus cellular process cellular response to mechanical stimulus cellular response to abiotic stimulus cellular response to external stimulus cellular response to environmental stimulus phosphorylation cellular metabolic process phosphate-containing compound metabolic process metabolic process phosphorus metabolic process regulation of biological process regulation of cellular process signaling biological regulation signal transduction intracellular signal transduction cell communication	intracellular anatomical structure cytoplasm cellular anatomical entity 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, B	IPR002893	Zinc finger, MYND-type	Domain
A, B	IPR046341	SET domain superfamily	Homologous Superfamily
A, B	IPR011990	Tetratricopeptide-like helical domain superfamily	Homologous Superfamily
A, B	IPR001214	SET domain	Domain
A, B	IPR044420	SMYD3, SET domain	Domain
A, B	IPR025805	Histone-lysine N-methyltransferase SMYD3	Family
C [auth I], D [auth J]	IPR017441	Protein kinase, ATP binding site	Binding Site
C [auth I], D [auth J]	IPR034879	Mitogen-activated protein kinase kinase kinase 2/3, PB1 domain	Domain
C [auth I], D [auth J]	IPR000270	PB1 domain	Domain
C [auth I], D [auth J]	IPR011009	Protein kinase-like domain superfamily	Homologous Superfamily
C [auth I], D [auth J]	IPR000719	Protein kinase domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B	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
C [auth I], D [auth J]	Pharos: Q9Y2U5	ovarian cancer pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia rheumatoid arthritis acute myeloid leukemia Blastic phase chronic myeloid leukemia glioblastoma interstitial lung disease lung large cell carcinoma malignant pancreatic neoplasm non-small cell lung carcinoma pancreatic ductal adenocarcinoma Pick disease tuberculosis astrocytic tumor idiopathic pulmonary fibrosis ovarian cancer pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia rheumatoid arthritis acute myeloid leukemia Blastic phase chronic myeloid leukemia glioblastoma interstitial lung disease lung large cell carcinoma malignant pancreatic neoplasm non-small cell lung carcinoma pancreatic ductal adenocarcinoma Pick disease tuberculosis astrocytic tumor idiopathic pulmonary fibrosis juvenile dermatomyositis malignant ependymoma medulloblastoma osteosarcoma pancreatic intraductal papillary-mucinous neoplasm primitive neuroectodermal tumor atypical teratoid rhabdoid tumor diabetes mellitus large cell medulloblastoma malignant glioma myopathy

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
C [auth I], D [auth J]	NH2	RESID: AA0081 , AA0083 , AA0084 , AA0086 , AA0087 , AA0088 , AA0090 , AA0091 , AA0092 , AA0093 , AA0095 , AA0096 , AA0097 , AA0098 , AA0099 , AA0100 PSI-MOD : L-alanine amide MOD:00090 , L-asparagine amide MOD:00092 , L-aspartic acid 1-amide MOD:00093 , L-glutamine amide MOD:00095 , L-glutamic acid 1-amide MOD:00096 , glycine amide MOD:00097 , L-isoleucine amide MOD:00099 , L-leucine amide MOD:00100 , L-lysine amide MOD:00101 , L-methionine amide MOD:00102 , L-proline amide MOD:00104 , L-serine amide MOD:00105 , L-threonine amide MOD:00106 , L-tryptophan amide MOD:00107 , L-tyrosine amide MOD:00108 , L-valine amide MOD:00109

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 R01GM133198.