Structure of PDB 5ytk Chain B Binding Site BS01

Receptor Information
>5ytk Chain B (length=274) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GKLSLQDVAELIRARACQRVVVMVGAGISTPSGIPDFRSPGSGLYSNLQQ
YDLPYPEAIFELPFFFHNPKPFFTLAKELYPGNYKPNVTHYFLRLLHDKG
LLLRLYTQNIDGLERVSGIPASKLVEAHGTFASATCTVCQRPFPGEDIRA
DVMADRVPRCPVCTGVVKPDIVFFGEPLPQRFLLHVVDFPMADLLLILGT
SLEVEPFASLTEAVRSSVPRLLINRDLVGPLAWHPRSRDVAQLGDVVHGV
ESLVELLGWTEEMRDLVQRETGKL
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 chain5ytk Chain B Residue 401 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB5ytk Sensing and Transmitting Intracellular Amino Acid Signals through Reversible Lysine Aminoacylations
Resolution2.7 Å
Binding residue
(original residue number in PDB)		C256 C259 C280
Binding residue
(residue number reindexed from 1)		C136 C139 C160
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) P155 D156 F157 R158 N229 D231 H248
Catalytic site (residue number reindexed from 1) P35 D36 F37 R38 N109 D111 H128
Enzyme Commision number 2.3.1.286: protein acetyllysine N-acetyltransferase.
Gene Ontology
Molecular Function
GO:0017136 NAD-dependent histone deacetylase activity
GO:0051287 NAD binding
GO:0070403 NAD+ binding

View graph for
Molecular Function
External links
PDB RCSB:5ytk, PDBe:5ytk, PDBj:5ytk
PDBsum5ytk
PubMed29198988
UniProtQ9NTG7|SIR3_HUMAN NAD-dependent protein deacetylase sirtuin-3, mitochondrial (Gene Name=SIRT3)

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