Structure of PDB 3tg5 Chain A

Receptor sequence

>3tg5A (length=425) Species: 9606 (Homo sapiens) [Search protein sequence]

LGGLERFCSPGKGRGLRALQPFQVGDLLFSCPAYAYVLTVNERGNHCEYC
FTRKEGLSKCGRCKQAFYCNVECQKEDWPMHKLECSPMVVFGENWNPSET
VRLTARILAKQKIHPERTPSEKLLAVKEFESHLDKLDNEKKDLIQSDIAA
LHHFYSKHLGFPDNDSLVVLFAQVNCNGFTIEDEELSHLGSAIFPDVALM
NHSCCPNVIVTYKGTLAEVRAVQEIKPGEEVFTSYIDLLYPTEDRNDRLR
DSYFFTCECQECTTKDKDKAKVEIRKLSDPPKAEAIRDMVRYARNVIEEF
RRAKHYKSPSELLEICELSQEKMSSVFEDSNVYMLHMMYQAMGVCLYMQD
WEGALQYGQKIIKPYSKHYPLYSLNVASMWLKLGRLYMGLEHKAAGEKAL
KKAIAIMEVAHGKDHPYISEIKQEI

3D structure

PDB

3tg5 Structure of human SMYD2 reveals the basis of p53 tumor suppressor methylation

Chain

Resolution

2.3 Å

3D
structure

[Spin on]
[Spin off]
[Reset orientation]

[High quality]
[Low quality]

[White background]
[Black background]

[Download]
[Download structure with residue number starting from 1]

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	peptide	A	C181 N182 G183 F184 T185 E187 S196 V215 Y240 I241 D242 Y245 R253 Y258 R306 H341 Y344 Q345 Y370 N380	C176 N177 G178 F179 T180 E182 S191 V210 Y235 I236 D237 Y240 R248 Y253 R301 H336 Y339 Q340 Y365 N375
BS02	SAH	A	K17 R19 H137 C181 A203 N206 H207 Y240 Y258 F260	K12 R14 H132 C176 A198 N201 H202 Y235 Y253 F255	BindingDB: IC50=180nM
BS03	ZN	A	C209 C262 C264 C267	C204 C257 C259 C262
BS04	ZN	A	C52 C74 C78	C47 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:3tg5, PDBe:3tg5, PDBj:3tg5
PDBsum	3tg5
PubMed	21880715
UniProt	Q9NRG4\|SMYD2_HUMAN N-lysine methyltransferase SMYD2 (Gene Name=SMYD2)

[Back to BioLiP]