Structure of PDB 5ex0 Chain A Binding Site BS03

Receptor Information
>5ex0 Chain A (length=429) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
FMEPLKVEKFATANRGNGLRAVTPLRPGELLFRSDPLAYTVCKGSRGVVC
DRCLLGKEKLMRCSQCRVAKYCSAKCQKKAWPDHKRECKCLKSCKPRYPP
DSVRLLGRVVFKLMDGAPSESEKLYSFYDLESNINKLTEDRKEGLRQLVM
TFQHFMREEIQDASQLPPAFDLFEAFAKVICNSFTICNAEMQEVGVGLYP
SISLLNHSCDPNCSIVFNGPHLLLRAVRDIEVGEELTICYLDMLMTSEER
RKQLRDQYCFECDCFRCQTQDKDADMLTGDEQVWKEVQESLKKIEELKAH
WKWEQVLAMCQAIISSNSERLPDINIYQLKVLDCAMDACINLGLLEEALF
YGTRTMEPYRIFFPGSHPVRGVQVMKVGKLQLHQGMFPQAMKNLRLAFDI
MRVTHGREHSLIEDLILLLEECDANIRAS
Ligand information
Ligand IDZN
InChIInChI=1S/Zn/q+2
InChIKeyPTFCDOFLOPIGGS-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.341[Zn++]
ACDLabs 10.04
OpenEye OEToolkits 1.5.0		[Zn+2]
FormulaZn
NameZINC ION
ChEMBLCHEMBL1236970
DrugBankDB14532
ZINC
PDB chain5ex0 Chain A Residue 502 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB5ex0 Structural Basis for Substrate Preference of SMYD3, a SET Domain-containing Protein Lysine Methyltransferase
Resolution2.7 Å
Binding residue
(original residue number in PDB)		C62 C65 H83 C87
Binding residue
(residue number reindexed from 1)		C63 C66 H84 C88
Annotation score1
Enzymatic activity
Enzyme Commision number 2.1.1.354: [histone H3]-lysine(4) N-trimethyltransferase.
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:5ex0, PDBe:5ex0, PDBj:5ex0
PDBsum5ex0
PubMed26929412
UniProtQ9H7B4|SMYD3_HUMAN Histone-lysine N-methyltransferase SMYD3 (Gene Name=SMYD3)

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