Structure of PDB 6ijl Chain A

Receptor sequence

>6ijlA (length=423) Species: 9606 (Homo sapiens) [Search protein sequence]

PLKVEKFATANRGNGLRAVTPLRPGELLFRSDPLAYTVCKGSRGVVCDRC
LLGKEKLMRCSQCRVAKYCSAKCQKKAWPDHKRECKCLKSCKPRYPPDSV
RLLGRVVFKLMDGAPSESEKLYSFYDLESNINKLTEDRKEGLRQLVMTFQ
HFMREEIQDASQLPPAFDLFEAFAKVICNSFTICNAEMQEVGVGLYPSIS
LLNHSCDPNCSIVFNGPHLLLRAVRDIEVGEELTICYLDMLMTSEERRKQ
LRDQYCFECDCFRCQTQDKDADMLTGDEQVWKEVQESLKKIEELKAHWKW
EQVLAMCQAIISSNSERLPDINIYQLKVLDCAMDACINLGLLEEALFYGT
RTMEPYRIFFPGSHPVRGVQVMKVGKLQLHQGMFPQAMKNLRLAFDIMRV
THGREHSLIEDLILLLEECDANI

3D structure

PDB

6ijl Discovery of Irreversible Inhibitors Targeting Histone Methyltransferase, SMYD3.

Chain

Resolution

2.351 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	A8U	A	F183 T184 C186 M190 I214 F216 Y239 Y257 D332 V368	F181 T182 C184 M188 I212 F214 Y237 Y255 D330 V366	PDBbind-CN: -logKd/Ki=7.93,IC50=11.7nM
BS02	ZN	A	C49 C52 C71 C75	C47 C50 C69 C73
BS03	ZN	A	C208 C263	C206 C261
BS04	ZN	A	C62 C65 H83	C60 C63 H81
BS05	SAM	A	R14 G15 N16 Y124 N132 C180 N181 S202 L203 N205 H206 Y239 Y257 F259	R12 G13 N14 Y122 N130 C178 N179 S200 L201 N203 H204 Y237 Y255 F257

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:6ijl, PDBe:6ijl, PDBj:6ijl
PDBsum	6ijl
PubMed	31223458
UniProt	Q9H7B4\|SMYD3_HUMAN Histone-lysine N-methyltransferase SMYD3 (Gene Name=SMYD3)

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