Structure of PDB 5d1b Chain A

Receptor sequence
>5d1bA (length=356) Species: 9606 (Homo sapiens) [Search protein sequence]
LVPVYIYSPEYVSMCDSLAKIPKRASMVHSLIEAYALHKQMRIVKPKVAS
MEEMATFHTDAYLQHLQKVSQEGEYGLGYDCPATEGIFDYAAAIGEATIT
AAQCLIDGMCKVAINWSGGWHHAKKDEASGFCYLNDAVLGILRLRRKFER
ILYVDLDLHHGDGVEDAFSFTSKVMTVSLHKFSPGFFPGTGDVSDVGLGK
GRYYSVNVPIQDGIQDEKYYQICESVLKEVYQAFNPKAVVLQLGADTIAG
DPMCSFNMTPVGIGKCLKYILQWQLATLILGGGGYNLANTARCWTYLTGV
ILGKTLSSEIPDHEFFTAYGPDYVLEITPSCRPDRNEPHRIQQILNYIKG
NLKHVV
3D structure
PDB5d1b Biochemical and Structural Characterization of HDAC8 Mutants Associated with Cornelia de Lange Syndrome Spectrum Disorders.
ChainA
Resolution2.9 Å
3D
structure
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Enzymatic activity
Enzyme Commision number 3.5.1.-
3.5.1.98: histone deacetylase.
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 ZN A D178 H180 D267 D157 H159 D246
BS02 TSN A H143 F152 D178 H180 Y306 H122 F131 D157 H159 Y285 BindingDB: IC50=90nM,Ki=45nM,Kd=3.9e+2nM
BS03 TSN A M274 Y306 M253 Y285 BindingDB: IC50=90nM,Ki=45nM,Kd=3.9e+2nM
Gene Ontology
Molecular Function
GO:0004407 histone deacetylase activity
GO:0005515 protein binding
GO:0016787 hydrolase activity
GO:0030544 Hsp70 protein binding
GO:0033558 protein lysine deacetylase activity
GO:0046872 metal ion binding
GO:0051879 Hsp90 protein binding
GO:0140297 DNA-binding transcription factor binding
GO:0160008 protein decrotonylase activity
GO:0160009 histone decrotonylase activity
Biological Process
GO:0000122 negative regulation of transcription by RNA polymerase II
GO:0006325 chromatin organization
GO:0007064 mitotic sister chromatid cohesion
GO:0031397 negative regulation of protein ubiquitination
GO:0031647 regulation of protein stability
GO:0032204 regulation of telomere maintenance
GO:0040029 epigenetic regulation of gene expression
Cellular Component
GO:0000118 histone deacetylase complex
GO:0000228 nuclear chromosome
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005694 chromosome
GO:0005737 cytoplasm

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:5d1b, PDBe:5d1b, PDBj:5d1b
PDBsum5d1b
PubMed26463496
UniProtQ9BY41|HDAC8_HUMAN Histone deacetylase 8 (Gene Name=HDAC8)

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