Structure of PDB 6z6o Chain J Binding Site BS01

Receptor Information
>6z6o Chain J (length=661) Species: 559292 (Saccharomyces cerevisiae S288C) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ENSLSTTSKSKRQVIVPVCMPKIHYSPLKTGLCYDVRMRYHAKIFTSYFE
YIDPHPEDPRRIYRIYKILAENGLINDPTLSGVDDLGDLMLKIPVRAATS
EEILEVHTKEHLEFIESTEKMSREELLKETEKGDSVYFNNDSYASARLPC
GGAIEACKAVVEGRVKNSLAVVRPPGHHAEPQAAGGFCLFSNVAVAAKNI
LKNYPESVRRIMILDWDIHHGNGTQKSFYQDDQVLYVSLHRFEMGKYYPG
TIQGQYDQTGEGKGEGFNCNITWPVGGVGDAEYMWAFEQVVMPMGREFKP
DLVIISSGFDAADGDTIGQCHVTPSCYGHMTHMLKSLARGNLCVVLEGGY
NLDAIARSALSVAKVLIGEPPDELPDPLSDPKPEVIEMIDKVIRLQSKYW
NCFRRRHANSGCNFNEPINDSIISKNFPLQKAIRQQQQHYLSDEFNFVTL
PLVSMDLPDNTVLCTPNISESNTIIIVVHDTSDIWAKRNVISGTIDLSSS
VIIDNSLDFIKWGLDRKYGIIDVNIPLTLFEPDNYSGMITSQEVLIYLWD
NYIKYFPSVAKIAFIGIGDSYSGIVHLLGHRDTRAVTKTVINFLGDKQLK
PLVPLVDETLSEWYFKNSLIFSNNSHQCKKFGRVLRCDTDLNNIIEERFE
EATDFILDSFE
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 chain6z6o Chain J Residue 801 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB6z6o Structural basis for the regulation of nucleosome recognition and HDAC activity by histone deacetylase assemblies.
Resolution3.8 Å
Binding residue
(original residue number in PDB)		D245 H247 D338
Binding residue
(residue number reindexed from 1)		D217 H219 D310
Annotation score1
Enzymatic activity
Enzyme Commision number 3.5.1.98: histone deacetylase.
Gene Ontology
Molecular Function
GO:0003682 chromatin binding
GO:0004407 histone deacetylase activity
GO:0005515 protein binding
GO:0008270 zinc ion binding
GO:0016787 hydrolase activity
GO:0042802 identical protein binding
Biological Process
GO:0000122 negative regulation of transcription by RNA polymerase II
GO:0006325 chromatin organization
GO:0006355 regulation of DNA-templated transcription
GO:0010621 negative regulation of transcription by transcription factor localization
GO:0040029 epigenetic regulation of gene expression
GO:0045944 positive regulation of transcription by RNA polymerase II
Cellular Component
GO:0000118 histone deacetylase complex
GO:0005634 nucleus
GO:0070823 HDA1 complex

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:6z6o, PDBe:6z6o, PDBj:6z6o
PDBsum6z6o
PubMed33523989
UniProtP53973|HDA1_YEAST Histone deacetylase HDA1 (Gene Name=HDA1)

[Back to BioLiP]