Structure of PDB 5v3h Chain A

Receptor sequence

>5v3hA (length=438) Species: 9606 (Homo sapiens) [Search protein sequence]

KDDDDKMRAEGLGGLERFCSPGKGRGLRALQPFQVGDLLFSCPAYAYVLT
VNERGNHCEYCFTRKEGLSKCGRCKQAFYCNVECQKEDWPMHKLECSPMV
VFGENWNPSETVRLTARILAKQKIHPERTPSEKLLAVKEFESHLDKLDNE
KKDLIQSDIAALHHFYSKHLGFPDNDSLVVLFAQVNCNGFTIEDEELSHL
GSAIFPDVALMNHSCCPNVIVTYKGTLAEVRAVQEIKPGEEVFTSYIDLL
YPTEDRNDRLRDSYFFTCECQECTTKDKDKAKVEIRKLSDPPKAEAIRDM
VRYARNVIEEFRRAKHYKSPSELLEICELSQEKMSSVFEDSNVYMLHMMY
QAMGVCLYMQDWEGALQYGQKIIKPYSKHYPLYSLNVASMWLKLGRLYMG
LEHKAAGEKALKKAIAIMEVAHGKDHPYISEIKQEIES

3D structure

PDB

5v3h Small molecule inhibitors and CRISPR/Cas9 mutagenesis demonstrate that SMYD2 and SMYD3 activity are dispensable for autonomous cancer cell proliferation.

Chain

Resolution

2.69 Å

3D
structure

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Enzymatic activity

Enzyme Commision number

2.1.1.-
2.1.1.354: [histone H3]-lysine(4) N-trimethyltransferase.

Interaction with ligand

Site #	Ligand	Ligand chain	Binding residues on receptor (original residue number in PDB)	Binding residues on receptor (residue number reindexed from 1)	Binding affinity
BS01	SAM	A	K17 R19 E135 H137 C181 A203 N206 H207 Y240 Y258 F260	K23 R25 E141 H143 C187 A209 N212 H213 Y246 Y264 F266
BS02	ZN	A	C209 C262 C264 C267	C215 C268 C270 C273
BS03	ZN	A	C52 C55 C74 C78	C58 C61 C80 C84
BS04	ZN	A	C65 C68 H86 C90	C71 C74 H92 C96
BS05	8WG	A	F184 T185 E187 D188 E189 Y240 Y258 L379 M412 H416	F190 T191 E193 D194 E195 Y246 Y264 L385 M418 H422	BindingDB: IC50=3.90nM
BS06	8WG	A	G183 S196 I241 D242 Y245 R253 H341	G189 S202 I247 D248 Y251 R259 H347	BindingDB: IC50=3.90nM

Gene Ontology

	Molecular Function
GO:0000993	RNA polymerase II complex binding
GO:0002039	p53 binding
GO:0005515	protein binding
GO:0008168	methyltransferase activity
GO:0016278	lysine N-methyltransferase activity
GO:0016279	protein-lysine N-methyltransferase activity
GO:0042054	histone methyltransferase activity
GO:0046872	metal ion binding
GO:0046975	histone H3K36 methyltransferase activity
GO:0140938	histone H3 methyltransferase activity
GO:0140999	histone H3K4 trimethyltransferase activity

	Biological Process
GO:0000122	negative regulation of transcription by RNA polymerase II
GO:0006325	chromatin organization
GO:0006338	chromatin remodeling
GO:0007507	heart development
GO:0008285	negative regulation of cell population proliferation
GO:0018026	peptidyl-lysine monomethylation
GO:0018027	peptidyl-lysine dimethylation
GO:0032259	methylation
GO:0043516	regulation of DNA damage response, signal transduction by p53 class mediator
GO:1901796	regulation of signal transduction by p53 class mediator

	Cellular Component
GO:0005634	nucleus
GO:0005654	nucleoplasm
GO:0005737	cytoplasm
GO:0005829	cytosol

View graph for
Molecular Function

View graph for
Biological Process

View graph for
Cellular Component

External links

PDB	RCSB:5v3h, PDBe:5v3h, PDBj:5v3h
PDBsum	5v3h
PubMed	29856759
UniProt	Q9NRG4\|SMYD2_HUMAN N-lysine methyltransferase SMYD2 (Gene Name=SMYD2)

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