Structure of PDB 8w9f Chain B Binding Site BS01

Receptor Information
>8w9f Chain B (length=385) Species: 4932 (Saccharomyces cerevisiae) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
VYEATPFDPITVKPSDKRRVAYFYDADVGNYAYGAGHPMKPHRIRMAHSL
IMNYGLYKKMEIYRAKPATKQEMCQFHTDEYIDFLSRVTPDNLEMFKRES
VKFNVGDDCPVFDGLYEYCSISGGGSMEGAARLNRGKCDVAVNYAGGLHH
AKKSEASGFCYLNDIVLGIIELLRYHPRVLYIDIDVHHGDGVEEAFYTTD
RVMTCSFHKYGEFFPGTGELRDIGVGAGKNYAVNVPLRDGIDDATYRSVF
EPVIKKIMEWYQPSAVVLQCGGDSLSGDRLGCFNLSMEGHANCVNYVKSF
GIPMMVVGGGGYTMRNVARTWCFETGLLNNVVLDKDLPYNEYYEYYGPDY
KLSVRPSNMFNVNTPEYLDKVMTNIFANLENTKYA
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 chain8w9f Chain B Residue 1000 [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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PDB8w9f Structures and dynamics of Rpd3S complex bound to nucleosome.
Resolution4.4 Å
Binding residue
(original residue number in PDB)		D186 H188
Binding residue
(residue number reindexed from 1)		D185 H187
Annotation score1
Enzymatic activity
Enzyme Commision number 3.5.1.98: histone deacetylase.
Gene Ontology
Molecular Function
GO:0003713 transcription coactivator activity
GO:0003714 transcription corepressor activity
GO:0004407 histone deacetylase activity
GO:0005515 protein binding
GO:0008270 zinc ion binding
GO:0016787 hydrolase activity
Biological Process
GO:0000082 G1/S transition of mitotic cell cycle
GO:0000086 G2/M transition of mitotic cell cycle
GO:0000122 negative regulation of transcription by RNA polymerase II
GO:0006325 chromatin organization
GO:0006334 nucleosome assembly
GO:0006355 regulation of DNA-templated transcription
GO:0006357 regulation of transcription by RNA polymerase II
GO:0006368 transcription elongation by RNA polymerase II
GO:0006979 response to oxidative stress
GO:0006995 cellular response to nitrogen starvation
GO:0016239 positive regulation of macroautophagy
GO:0016479 negative regulation of transcription by RNA polymerase I
GO:0030174 regulation of DNA-templated DNA replication initiation
GO:0031507 heterochromatin formation
GO:0034503 protein localization to nucleolar rDNA repeats
GO:0034605 cellular response to heat
GO:0044804 nucleophagy
GO:0045128 negative regulation of reciprocal meiotic recombination
GO:0045944 positive regulation of transcription by RNA polymerase II
GO:0051321 meiotic cell cycle
GO:0061186 negative regulation of silent mating-type cassette heterochromatin formation
GO:0061188 negative regulation of rDNA heterochromatin formation
GO:0070550 rDNA chromatin condensation
Cellular Component
GO:0000118 histone deacetylase complex
GO:0005634 nucleus
GO:0005737 cytoplasm
GO:0032221 Rpd3S complex
GO:0033698 Rpd3L complex
GO:0034399 nuclear periphery
GO:0070210 Rpd3L-Expanded complex
GO:0070211 Snt2C complex
GO:0070822 Sin3-type complex

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:8w9f, PDBe:8w9f, PDBj:8w9f
PDBsum8w9f
PubMed38598631
UniProtP32561|RPD3_YEAST Histone deacetylase RPD3 (Gene Name=RPD3)

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