Structure of PDB 5kjn Chain A

Receptor sequence

>5kjnA (length=429) Species: 9606 (Homo sapiens) [Search protein sequence]

GLGGLERFCSPGKGRGLRALQPFQVGDLLFSCPAYAYVLTVNERGNHCEY
CFTRKEGLSKCGRCKQAFYCNVECQKEDWPMHKLECSPMVVFGENWNPSE
TVRLTARILAKQKIHPERTPSEKLLAVKEFESHLDKLDNEKKDLIQSDIA
ALHHFYSKHLEFPDNDSLVVLFAQVNCNGFTIEDEELSHLGSAIFPDVAL
MNHSCCPNVIVTYKGTLAEVRAVQEIKPGEEVFTSYIDLLYPTEDRNDRL
RDSYFFTCECQECTTKDKDKAKVEIRKLSDPPKAEAIRDMVRYARNVIEE
FRRAKHYKSPSELLEICELSQEKMSSVFEDSNVYMLHMMYQAMGVCLYMQ
DWEGALQYGQKIIKPYSKHYPLYSLNVASMWLKLGRLYMGLEHKAAGEKA
LKKAIAIMEVAHGKDHPYISEIKQEIESH

3D structure

PDB

5kjn Design, Synthesis, and Biological Activity of Substrate Competitive SMYD2 Inhibitors.

Chain

Resolution

2.72 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 N182 A203 N206 H207 Y240 Y258 F260	K13 R15 E131 H133 N178 A199 N202 H203 Y236 Y254 F256
BS02	BU3	A	Y39 K115	Y35 K111
BS03	BU3	A	W356 G394	W352 G390
BS04	BU3	A	R122 T123 P124 K127	R118 T119 P120 K123
BS05	BU3	A	R67 W83	R63 W79
BS06	BU3	A	D188 E190	D184 E186
BS07	6TL	A	K145 I149 V179 N180 N182 G183 F184 T185 Y240 S257 Y258 F259	K141 I145 V175 N176 N178 G179 F180 T181 Y236 S253 Y254 F255	PDBbind-CN: -logKd/Ki=7.77,IC50=0.017uM
BS08	ZN	A	C52 C74 C78	C48 C70 C74
BS09	ZN	A	C65 C68 H86 C90	C61 C64 H82 C86
BS10	ZN	A	C209 C262 C264 C267	C205 C258 C260 C263

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

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Biological Process

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Cellular Component

External links

PDB	RCSB:5kjn, PDBe:5kjn, PDBj:5kjn
PDBsum	5kjn
PubMed	28002961
UniProt	Q9NRG4\|SMYD2_HUMAN N-lysine methyltransferase SMYD2 (Gene Name=SMYD2)

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