Structure of PDB 5ex0 Chain A

Receptor sequence

>5ex0A (length=429) Species: 9606 (Homo sapiens) [Search protein sequence]

FMEPLKVEKFATANRGNGLRAVTPLRPGELLFRSDPLAYTVCKGSRGVVC
DRCLLGKEKLMRCSQCRVAKYCSAKCQKKAWPDHKRECKCLKSCKPRYPP
DSVRLLGRVVFKLMDGAPSESEKLYSFYDLESNINKLTEDRKEGLRQLVM
TFQHFMREEIQDASQLPPAFDLFEAFAKVICNSFTICNAEMQEVGVGLYP
SISLLNHSCDPNCSIVFNGPHLLLRAVRDIEVGEELTICYLDMLMTSEER
RKQLRDQYCFECDCFRCQTQDKDADMLTGDEQVWKEVQESLKKIEELKAH
WKWEQVLAMCQAIISSNSERLPDINIYQLKVLDCAMDACINLGLLEEALF
YGTRTMEPYRIFFPGSHPVRGVQVMKVGKLQLHQGMFPQAMKNLRLAFDI
MRVTHGREHSLIEDLILLLEECDANIRAS

3D structure

PDB

5ex0 Structural Basis for Substrate Preference of SMYD3, a SET Domain-containing Protein Lysine Methyltransferase

Chain

Resolution

2.7 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

2.1.1.354: [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)
BS01	peptide	A	S101 S182 F183 T184 E192 Y239 D241 M244 Q252 Q256 Y257 E294	S102 S183 F184 T185 E193 Y240 D242 M245 Q253 Q257 Y258 E295
BS02	ZN	A	C49 C52 C71 C75	C50 C53 C72 C76
BS03	ZN	A	C62 C65 H83 C87	C63 C66 H84 C88
BS04	ZN	A	C208 C261 C263 C266	C209 C262 C264 C267
BS05	SAH	A	R14 N16 Y124 N132 S202 N205 H206 Y239 Y257 F259	R15 N17 Y125 N133 S203 N206 H207 Y240 Y258 F260

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

View graph for
Molecular Function

View graph for
Biological Process

View graph for
Cellular Component

External links

PDB	RCSB:5ex0, PDBe:5ex0, PDBj:5ex0
PDBsum	5ex0
PubMed	26929412
UniProt	Q9H7B4\|SMYD3_HUMAN Histone-lysine N-methyltransferase SMYD3 (Gene Name=SMYD3)

[Back to BioLiP]