Structure of PDB 5arf Chain A

Receptor sequence

>5arfA (length=425) Species: 9606 (Homo sapiens) [Search protein sequence]

LGGLERFCSPGKGRGLRALQPFQVGDLLFSCPAYAYVLTVNERGNHCEYC
FTRKEGLSKCGRCKQAFYCNVECQKEDWPMHKLECSPMVVFGENWNPSET
VRLTARILAKQKIHPERTPSEKLLAVKEFESHLDKLDNEKKDLIQSDIAA
LHHFYSKHLGFPDNDSLVVLFAQVNCNGFTIEDEELSHLGSAIFPDVALM
NHSCCPNVIVTYKGTLAEVRAVQEIKPGEEVFTSYIDLLYPTEDRNDRLR
DSYFFTCECQECTTKDKDKAKVEIRKLSDPPKAEAIRDMVRYARNVIEEF
RRAKHYKSPSELLEICELSQEKMSSVFEDSNVYMLHMMYQAMGVCLYMQD
WEGALQYGQKIIKPYSKHYPLYSLNVASMWLKLGRLYMGLEHKAAGEKAL
KKAIAIMEVAHGKDHPYISEIKQEI

3D structure

PDB

5arf Discovery and Characterization of a Highly Potent and Selective Aminopyrazoline-Based in Vivo Probe (Bay-598) for the Protein Lysine Methyltransferase Smyd2.

Chain

Resolution

1.92 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	I9H	A	E104 T105 L108 G183 F184 T185 S196 Y217 Y240 Y258	E99 T100 L103 G178 F179 T180 S191 Y212 Y235 Y253	MOAD: Kd=540nM PDBbind-CN: -logKd/Ki=6.27,Kd=540nM
BS02	SAM	A	K17 R19 E135 H137 C181 N182 A203 L204 N206 H207 Y240 Y258 F260	K12 R14 E130 H132 C176 N177 A198 L199 N201 H202 Y235 Y253 F255
BS03	ZN	A	C209 C262 C264 C267	C204 C257 C259 C262
BS04	ZN	A	C52 C55 C74 C78	C47 C50 C69 C73
BS05	ZN	A	C65 C68 H86 C90	C60 C63 H81 C85

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:5arf, PDBe:5arf, PDBj:5arf
PDBsum	5arf
PubMed	27075367
UniProt	Q9NRG4\|SMYD2_HUMAN N-lysine methyltransferase SMYD2 (Gene Name=SMYD2)

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