Structure of PDB 6z2k Chain K

Receptor sequence

>6z2kK (length=369) Species: 9606 (Homo sapiens) [Search protein sequence]

RRKVCYYYDGDVGNYYYGQGHPMKPHRIRMTHNLLLNYGLYRKMEIYRPH
KANAEEMTKYHSDDYIKFLRSIRPDNMSEYSKQMQRFNVGEDCPVFDGLF
EFCQLSTGGSVASAVKLNKQQTDIAVNWAGGLHHAKKSEASGFCYVNDIV
LAILELLKYHQRVLYIDIDIHHGDGVEEAFYTTDRVMTVSFHKYGEYFPG
TGDLRDIGAGKGKYYAVNYPLRDGIDDESYEAIFKPVMSKVMEMFQPSAV
VLQCGSDSLSGDRLGCFNLTIKGHAKCVEFVKSFNLPMLMLGGGGYTIRN
VARCWTYETAVALDTEIPNELPYNDYFEYFGPDFKLHISPSNMTNQNTNE
YLEKIKQRLFENLRMLPHA

3D structure

PDB

6z2k The MiDAC histone deacetylase complex is essential for embryonic development and has a unique multivalent structure.

Chain

Resolution

4.5 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	K	D176 H178 D264	D169 H171 D257

Gene Ontology

	Molecular Function
GO:0000976	transcription cis-regulatory region binding
GO:0000978	RNA polymerase II cis-regulatory region sequence-specific DNA binding
GO:0000979	RNA polymerase II core promoter sequence-specific DNA binding
GO:0001046	core promoter sequence-specific DNA binding
GO:0001222	transcription corepressor binding
GO:0002039	p53 binding
GO:0003677	DNA binding
GO:0003682	chromatin binding
GO:0003714	transcription corepressor activity
GO:0004407	histone deacetylase activity
GO:0005515	protein binding
GO:0016787	hydrolase activity
GO:0019899	enzyme binding
GO:0031492	nucleosomal DNA binding
GO:0033558	protein lysine deacetylase activity
GO:0035851	Krueppel-associated box domain binding
GO:0042826	histone deacetylase binding
GO:0051059	NF-kappaB binding
GO:0061629	RNA polymerase II-specific DNA-binding transcription factor binding
GO:0070888	E-box binding
GO:0140297	DNA-binding transcription factor binding
GO:0160008	protein decrotonylase activity
GO:0160009	histone decrotonylase activity
GO:1990841	promoter-specific chromatin binding

	Biological Process
GO:0000122	negative regulation of transcription by RNA polymerase II
GO:0006325	chromatin organization
GO:0006338	chromatin remodeling
GO:0006346	DNA methylation-dependent heterochromatin formation
GO:0006357	regulation of transcription by RNA polymerase II
GO:0006476	protein deacetylation
GO:0007492	endoderm development
GO:0007623	circadian rhythm
GO:0008284	positive regulation of cell population proliferation
GO:0009913	epidermal cell differentiation
GO:0010628	positive regulation of gene expression
GO:0010629	negative regulation of gene expression
GO:0010832	negative regulation of myotube differentiation
GO:0021766	hippocampus development
GO:0030182	neuron differentiation
GO:0030336	negative regulation of cell migration
GO:0030512	negative regulation of transforming growth factor beta receptor signaling pathway
GO:0031507	heterochromatin formation
GO:0032922	circadian regulation of gene expression
GO:0036120	cellular response to platelet-derived growth factor stimulus
GO:0042475	odontogenesis of dentin-containing tooth
GO:0042659	regulation of cell fate specification
GO:0042733	embryonic digit morphogenesis
GO:0043066	negative regulation of apoptotic process
GO:0043124	negative regulation of canonical NF-kappaB signal transduction
GO:0043922	negative regulation by host of viral transcription
GO:0045814	negative regulation of gene expression, epigenetic
GO:0045892	negative regulation of DNA-templated transcription
GO:0045893	positive regulation of DNA-templated transcription
GO:0045944	positive regulation of transcription by RNA polymerase II
GO:0048511	rhythmic process
GO:0048661	positive regulation of smooth muscle cell proliferation
GO:0048709	oligodendrocyte differentiation
GO:0048714	positive regulation of oligodendrocyte differentiation
GO:0060766	negative regulation of androgen receptor signaling pathway
GO:0060789	hair follicle placode formation
GO:0061029	eyelid development in camera-type eye
GO:0061198	fungiform papilla formation
GO:0090090	negative regulation of canonical Wnt signaling pathway
GO:1902455	negative regulation of stem cell population maintenance
GO:1902459	positive regulation of stem cell population maintenance
GO:2000273	positive regulation of signaling receptor activity
GO:2000736	regulation of stem cell differentiation
GO:2001243	negative regulation of intrinsic apoptotic signaling pathway

	Cellular Component
GO:0000118	histone deacetylase complex
GO:0000785	chromatin
GO:0000792	heterochromatin
GO:0005634	nucleus
GO:0005654	nucleoplasm
GO:0005667	transcription regulator complex
GO:0005737	cytoplasm
GO:0005829	cytosol
GO:0016581	NuRD complex
GO:0017053	transcription repressor complex
GO:0032991	protein-containing complex
GO:0043025	neuronal cell body
GO:0070822	Sin3-type complex

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Molecular Function

View graph for
Biological Process

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Cellular Component

External links

PDB	RCSB:6z2k, PDBe:6z2k, PDBj:6z2k
PDBsum	6z2k
PubMed	32591534
UniProt	Q13547\|HDAC1_HUMAN Histone deacetylase 1 (Gene Name=HDAC1)

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