Structure of PDB 5kjm Chain A

Receptor sequence
>5kjmA (length=429) Species: 9606 (Homo sapiens) [Search protein sequence]
GLGGLERFCSPGKGRGLRALQPFQVGDLLFSCPAYAYVLTVNERGNHCEY
CFTRKEGLSKCGRCKQAFYCNVECQKEDWPMHKLECSPMVVFGENWNPSE
TVRLTARILAKQKIHPERTPSEKLLAVKEFESHLDKLDNEKKDLIQSDIA
ALHHFYSKHLEFPDNDSLVVLFAQVNCNGFTIEDEELSHLGSAIFPDVAL
MNHSCCPNVIVTYKGTLAEVRAVQEIKPGEEVFTSYIDLLYPTEDRNDRL
RDSYFFTCECQECTTKDKDKAKVEIRKLSDPPKAEAIRDMVRYARNVIEE
FRRAKHYKSPSELLEICELSQEKMSSVFEDSNVYMLHMMYQAMGVCLYMQ
DWEGALQYGQKIIKPYSKHYPLYSLNVASMWLKLGRLYMGLEHKAAGEKA
LKKAIAIMEVAHGKDHPYISEIKQEIESH
3D structure
PDB5kjm Design, Synthesis, and Biological Activity of Substrate Competitive SMYD2 Inhibitors.
ChainA
Resolution2.19 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 N182 A203 N206 H207 Y240 Y258 F260 K13 R15 E131 H133 C177 N178 A199 N202 H203 Y236 Y254 F256
BS02 6TM A K145 I149 N180 N182 G183 F184 T185 Y240 Y258 K141 I145 N176 N178 G179 F180 T181 Y236 Y254 MOAD: ic50=0.065uM
PDBbind-CN: -logKd/Ki=7.19,IC50=0.065uM
BS03 ZN A C52 C74 C78 C48 C70 C74
BS04 ZN A C65 C68 H86 C90 C61 C64 H82 C86
BS05 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

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:5kjm, PDBe:5kjm, PDBj:5kjm
PDBsum5kjm
PubMed28002961
UniProtQ9NRG4|SMYD2_HUMAN N-lysine methyltransferase SMYD2 (Gene Name=SMYD2)

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