Structure of PDB 8of4 Chain L Binding Site BS01

Receptor Information
>8of4 Chain L (length=237) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
PPEELERKVWELARLVWQSSSVVFHTGAGISTASGITFESARPTQTHMAL
VQLERVGLLRFLVSQNVDGLHVRSGFPRDKLAELHGNMFVEECAKCKTQY
VRDTVVGTMGLKATGRLCTVAKARGLRACRGELRDTILDWEDSLPDRDLA
LADEASRNADLSITLGTSLQIRPSGNLPLATKRRGGRLVIVNLQPTKHDR
HADLRIHGYVDEVMTRLMKHLGLEIPAWDGPRVLERA
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 chain8of4 Chain L Residue 401 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB8of4 Binding to nucleosome poises SIRT6 for histone H3 de-acetylation
Resolution2.94 Å
Binding residue
(original residue number in PDB)		C141 C144 C177
Binding residue
(residue number reindexed from 1)		C93 C96 C129
Annotation score1
Enzymatic activity
Enzyme Commision number 2.3.1.-
2.3.1.286: protein acetyllysine N-acetyltransferase.
2.4.2.-
Gene Ontology
Molecular Function
GO:0003677 DNA binding
GO:0003682 chromatin binding
GO:0003684 damaged DNA binding
GO:0003714 transcription corepressor activity
GO:0003723 RNA binding
GO:0003950 NAD+-protein poly-ADP-ribosyltransferase activity
GO:0005515 protein binding
GO:0008270 zinc ion binding
GO:0016746 acyltransferase activity
GO:0016757 glycosyltransferase activity
GO:0016779 nucleotidyltransferase activity
GO:0017136 NAD-dependent histone deacetylase activity
GO:0031490 chromatin DNA binding
GO:0031491 nucleosome binding
GO:0032129 histone H3K9 deacetylase activity
GO:0034979 NAD-dependent protein lysine deacetylase activity
GO:0042803 protein homodimerization activity
GO:0046872 metal ion binding
GO:0046969 NAD-dependent histone H3K9 deacetylase activity
GO:0070403 NAD+ binding
GO:0097372 NAD-dependent histone H3K18 deacetylase activity
GO:0106222 lncRNA binding
GO:0106274 NAD+-protein-arginine ADP-ribosyltransferase activity
GO:0140612 DNA damage sensor activity
GO:0140765 NAD-dependent histone H3K56 deacetylase activity
GO:0140773 NAD-dependent protein demyristoylase activity
GO:0140774 NAD-dependent protein depalmitoylase activity
GO:0140804 NAD+-protein-lysine ADP-ribosyltransferase activity
GO:1904841 TORC2 complex binding
GO:1990404 NAD+-protein ADP-ribosyltransferase activity
Biological Process
GO:0000122 negative regulation of transcription by RNA polymerase II
GO:0006281 DNA repair
GO:0006284 base-excision repair
GO:0006302 double-strand break repair
GO:0006325 chromatin organization
GO:0006338 chromatin remodeling
GO:0006476 protein deacetylation
GO:0006606 protein import into nucleus
GO:0008285 negative regulation of cell population proliferation
GO:0008340 determination of adult lifespan
GO:0009411 response to UV
GO:0010526 retrotransposon silencing
GO:0010569 regulation of double-strand break repair via homologous recombination
GO:0019216 regulation of lipid metabolic process
GO:0031508 pericentric heterochromatin formation
GO:0031509 subtelomeric heterochromatin formation
GO:0031648 protein destabilization
GO:0032024 positive regulation of insulin secretion
GO:0032206 positive regulation of telomere maintenance
GO:0032436 positive regulation of proteasomal ubiquitin-dependent protein catabolic process
GO:0032922 circadian regulation of gene expression
GO:0034244 negative regulation of transcription elongation by RNA polymerase II
GO:0042181 ketone biosynthetic process
GO:0042308 negative regulation of protein import into nucleus
GO:0042593 glucose homeostasis
GO:0042752 regulation of circadian rhythm
GO:0043687 post-translational protein modification
GO:0045600 positive regulation of fat cell differentiation
GO:0045721 negative regulation of gluconeogenesis
GO:0045814 negative regulation of gene expression, epigenetic
GO:0045820 negative regulation of glycolytic process
GO:0045892 negative regulation of DNA-templated transcription
GO:0046325 negative regulation of D-glucose import
GO:0046827 positive regulation of protein export from nucleus
GO:0048146 positive regulation of fibroblast proliferation
GO:0050708 regulation of protein secretion
GO:0050994 regulation of lipid catabolic process
GO:0051697 protein delipidation
GO:0055007 cardiac muscle cell differentiation
GO:0120162 positive regulation of cold-induced thermogenesis
GO:0120186 negative regulation of protein localization to chromatin
GO:0120187 positive regulation of protein localization to chromatin
GO:0140861 DNA repair-dependent chromatin remodeling
GO:1902459 positive regulation of stem cell population maintenance
GO:1902732 positive regulation of chondrocyte proliferation
GO:1903076 regulation of protein localization to plasma membrane
GO:1905555 positive regulation of blood vessel branching
GO:1905564 positive regulation of vascular endothelial cell proliferation
GO:1990166 protein localization to site of double-strand break
GO:2000648 positive regulation of stem cell proliferation
GO:2000738 positive regulation of stem cell differentiation
GO:2000773 negative regulation of cellular senescence
GO:2000781 positive regulation of double-strand break repair
Cellular Component
GO:0000781 chromosome, telomeric region
GO:0000785 chromatin
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005694 chromosome
GO:0005721 pericentric heterochromatin
GO:0005730 nucleolus
GO:0005783 endoplasmic reticulum
GO:0035861 site of double-strand break
GO:0043231 intracellular membrane-bounded organelle
GO:0090734 site of DNA damage
GO:0099115 chromosome, subtelomeric region

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:8of4, PDBe:8of4, PDBj:8of4
PDBsum8of4
PubMed38415718
UniProtQ8N6T7|SIR6_HUMAN NAD-dependent protein deacylase sirtuin-6 (Gene Name=SIRT6)

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