Structure of PDB 6cby Chain B

Receptor sequence
>6cbyB (length=422) Species: 9606 (Homo sapiens) [Search protein sequence]
GLGGLERFCSPGKGRGLRALQPFQVGDLLFSCPAYAYVLTVNERGNHCEY
CFTRKEGLSKCGRCKQAFYCNVECQKEDWPMHKLECSPMVVFGENWNPSE
TVRLTARILAKQKIHPERTPSEKLLAVKEFESHLDKLDNEKKDLIQSDIA
ALHHFYSKHLEFPDNDSLVVLFAQVNCNGFTIEDEELSHLGSAIFPDVAL
MNHSCCPNVIVTYKGTLAEVRAVQEIKPGEEVFTSYIDLLYPTEDRNDRL
RDSYFFTCECQECTTKDKDKAKVEIKAEAIRDMVRYARNVIEEFRRAKHY
KSPSELLEICELSQEKMSSVFEDSNVYMLHMMYQAMGVCLYMQDWEGALQ
YGQKIIKPYSKHYPLYSLNVASMWLKLGRLYMGLEHKAAGEKALKKAIAI
MEVAHGKDHPYISEIKQEIESH
3D structure
PDB6cby Crystal structure of human SET and MYND Domain Containing protein 2 with MTF9975
ChainB
Resolution2.55 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 ZN B C52 C74 C78 C48 C70 C74
BS02 ZN B C65 C68 H86 C90 C61 C64 H82 C86
BS03 ZN B C209 C262 C264 C267 C205 C258 C260 C263
BS04 EW4 B K17 H137 C181 N182 F184 N206 H207 Y240 Y258 F260 E263 K13 H133 C177 N178 F180 N202 H203 Y236 Y254 F256 E259 BindingDB: IC50=1300nM
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:6cby, PDBe:6cby, PDBj:6cby
PDBsum6cby
PubMed31415173
UniProtQ9NRG4|SMYD2_HUMAN N-lysine methyltransferase SMYD2 (Gene Name=SMYD2)

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