Structure of PDB 5d1d Chain A Binding Site BS01

Receptor Information
>5d1d Chain A (length=364) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
LVPVYIYSPEYVSMCDSLAKIPKRASMVHSLIEAYALHKQMRIVKPKVAS
MEEMATFHTDAYLQHLQKVSQEGDDDHLDSIEYGLGYDCPATEGIFDYAA
AIGGATITAAQCLIDGMCKVAINWSGGWHHAKKDEASGFCYLNDAVLGIL
RLRRKFERILYVDLDLHHGDGVEDAFSFTSKVMTVSLHKFSPGFFPGTGD
VSDVGLGKGRYYSVNVPIQDGIQDEKYYQICESVLKEVYQAFNPKAVVLQ
LGADTIAGDPMCSFNMTPVGIGKCLKYILQWQLATLILGGGGFNLANTAR
CWTYLTGVILGKTLSSEIPDHEFFTAYGPDYVLEITPSCRPDRNEPHRIQ
QILNYIKGNLKHVV
Ligand information
Receptor-Ligand Complex Structure
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PDB5d1d Biochemical and Structural Characterization of HDAC8 Mutants Associated with Cornelia de Lange Syndrome Spectrum Disorders.
Resolution2.011 Å
Binding residue
(original residue number in PDB)		K33 Y100 D101 W141 E148 G151 F152 H180 F208 P209 G304 F306
Binding residue
(residue number reindexed from 1)		K20 Y87 D88 W128 E135 G138 F139 H167 F195 P196 G291 F293
Enzymatic activity
Enzyme Commision number 3.5.1.-
3.5.1.98: histone deacetylase.
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:5d1d, PDBe:5d1d, PDBj:5d1d
PDBsum5d1d
PubMed26463496
UniProtQ9BY41|HDAC8_HUMAN Histone deacetylase 8 (Gene Name=HDAC8)

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