Structure of PDB 5xxd Chain A

Receptor sequence

>5xxdA (length=423) Species: 9606 (Homo sapiens) [Search protein sequence]

PLKVEKFATANRGNGLRAVTPLRPGELLFRSDPLAYTVCKGSRGVVCDRC
LLGKEKLMRCSQCRVAKYCSAKCQKKAWPDHKRECKCLKSCKPRYPPDSV
RLLGRVVFKLMDGAPSESEKLYSFYDLESNINKLTEDRKEGLRQLVMTFQ
HFMREEIQDASQLPPAFDLFEAFAKVICNSFTICNAEMQEVGVGLYPSIS
LLNHSCDPNCSIVFNGPHLLLRAVRDIEVGEELTICYLDMLMTSEERRKQ
LRDQYCFECDCFRCQTQDKDADMLTGDEQVWKEVQESLKKIEELKAHWKW
EQVLAMCQAIISSNSERLPDINIYQLKVLDCAMDACINLGLLEEALFYGT
RTMEPYRIFFPGSHPVRGVQVMKVGKLQLHQGMFPQAMKNLRLAFDIMRV
THGREHSLIEDLILLLEECDANI

3D structure

PDB

5xxd Crystal structure of SmyD3 in complex with covalent inhibitor 1

Chain

Resolution

2.314 Å

3D
structure

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Enzymatic activity

Enzyme Commision number

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	R14 N16 Y124 N132 N181 S202 L203 N205 H206 Y239 Y257 F259	R12 N14 Y122 N130 N179 S200 L201 N203 H204 Y237 Y255 F257
BS02	ZN	A	C208 C261 C263 C266	C206 C259 C261 C264
BS03	ZN	A	C62 C65 H83 C87	C60 C63 H81 C85
BS04	ZN	A	C49 C52 C71 C75	C47 C50 C69 C73
BS05	8NR	A	N181 S182 F183 T184 C186 M190 I237 Y239 Y257	N179 S180 F181 T182 C184 M188 I235 Y237 Y255	BindingDB: IC50=>750000nM

Gene Ontology

	Molecular Function
GO:0000978	RNA polymerase II cis-regulatory region sequence-specific DNA binding
GO:0000993	RNA polymerase II complex binding
GO:0001162	RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding
GO:0005515	protein binding
GO:0008168	methyltransferase activity
GO:0042054	histone methyltransferase activity
GO:0046872	metal ion binding
GO:0140939	histone H4 methyltransferase activity
GO:0140954	histone H3K36 dimethyltransferase activity
GO:0140999	histone H3K4 trimethyltransferase activity

	Biological Process
GO:0006325	chromatin organization
GO:0006334	nucleosome assembly
GO:0014904	myotube cell development
GO:0032259	methylation
GO:0045184	establishment of protein localization
GO:0045944	positive regulation of transcription by RNA polymerase II
GO:0071549	cellular response to dexamethasone stimulus

	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:5xxd, PDBe:5xxd, PDBj:5xxd
PDBsum	5xxd
PubMed
UniProt	Q9H7B4\|SMYD3_HUMAN Histone-lysine N-methyltransferase SMYD3 (Gene Name=SMYD3)

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