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SummaryStructural detailsExperimental detailsFunctional detailsSequence NeighborHistoryDownloads

9R4I

An auto inhibitory loop in the MiDAC histone deacetylase complex

Functional Information from GO Data
ChainGOidnamespacecontents
A0000118cellular_componenthistone deacetylase complex
A0000122biological_processnegative regulation of transcription by RNA polymerase II
A0000785cellular_componentchromatin
A0000792cellular_componentheterochromatin
A0000976molecular_functiontranscription cis-regulatory region binding
A0000978molecular_functionRNA polymerase II cis-regulatory region sequence-specific DNA binding
A0000979molecular_functionRNA polymerase II core promoter sequence-specific DNA binding
A0001046molecular_functioncore promoter sequence-specific DNA binding
A0001222molecular_functiontranscription corepressor binding
A0002039molecular_functionp53 binding
A0003677molecular_functionDNA binding
A0003682molecular_functionchromatin binding
A0003714molecular_functiontranscription corepressor activity
A0004407molecular_functionhistone deacetylase activity
A0005515molecular_functionprotein binding
A0005634cellular_componentnucleus
A0005654cellular_componentnucleoplasm
A0005667cellular_componenttranscription regulator complex
A0005737cellular_componentcytoplasm
A0005829cellular_componentcytosol
A0006325biological_processchromatin organization
A0006338biological_processchromatin remodeling
A0006346biological_processDNA methylation-dependent constitutive heterochromatin formation
A0006357biological_processregulation of transcription by RNA polymerase II
A0007623biological_processcircadian rhythm
A0008284biological_processpositive regulation of cell population proliferation
A0009913biological_processepidermal cell differentiation
A0010628biological_processpositive regulation of gene expression
A0010629biological_processnegative regulation of gene expression
A0010832biological_processnegative regulation of myotube differentiation
A0016581cellular_componentNuRD complex
A0016811molecular_functionhydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides
A0017053cellular_componenttranscription repressor complex
A0019899molecular_functionenzyme binding
A0030336biological_processnegative regulation of cell migration
A0030512biological_processnegative regulation of transforming growth factor beta receptor signaling pathway
A0031492molecular_functionnucleosomal DNA binding
A0031507biological_processheterochromatin formation
A0032922biological_processcircadian regulation of gene expression
A0032991cellular_componentprotein-containing complex
A0033148biological_processpositive regulation of intracellular estrogen receptor signaling pathway
A0033558molecular_functionprotein lysine deacetylase activity
A0035851molecular_functionKrueppel-associated box domain binding
A0036120biological_processcellular response to platelet-derived growth factor stimulus
A0042475biological_processodontogenesis of dentin-containing tooth
A0042659biological_processregulation of cell fate specification
A0042733biological_processembryonic digit morphogenesis
A0042826molecular_functionhistone deacetylase binding
A0043025cellular_componentneuronal cell body
A0043066biological_processnegative regulation of apoptotic process
A0043922biological_processhost-mediated suppression of viral transcription
A0045814biological_processnegative regulation of gene expression, epigenetic
A0045892biological_processnegative regulation of DNA-templated transcription
A0045893biological_processpositive regulation of DNA-templated transcription
A0045944biological_processpositive regulation of transcription by RNA polymerase II
A0045995biological_processregulation of embryonic development
A0048661biological_processpositive regulation of smooth muscle cell proliferation
A0051059molecular_functionNF-kappaB binding
A0060766biological_processnegative regulation of androgen receptor signaling pathway
A0060789biological_processhair follicle placode formation
A0061029biological_processeyelid development in camera-type eye
A0061198biological_processfungiform papilla formation
A0061629molecular_functionRNA polymerase II-specific DNA-binding transcription factor binding
A0070822cellular_componentSin3-type complex
A0070888molecular_functionE-box binding
A0090090biological_processnegative regulation of canonical Wnt signaling pathway
A0140297molecular_functionDNA-binding transcription factor binding
A0141221molecular_functionhistone deacetylase activity, hydrolytic mechanism
A0160008molecular_functionprotein decrotonylase activity
A0160009molecular_functionhistone decrotonylase activity
A0160216molecular_functionprotein lysine delactylase activity
A1902455biological_processnegative regulation of stem cell population maintenance
A1902459biological_processpositive regulation of stem cell population maintenance
A1990841molecular_functionpromoter-specific chromatin binding
A1990904cellular_componentribonucleoprotein complex
A2000736biological_processregulation of stem cell differentiation
C0000118cellular_componenthistone deacetylase complex
C0003677molecular_functionDNA binding
C0005515molecular_functionprotein binding
C0005634cellular_componentnucleus
C0005654cellular_componentnucleoplasm
C0005694cellular_componentchromosome
C0005730cellular_componentnucleolus
C0006325biological_processchromatin organization
C0031491molecular_functionnucleosome binding
C0042803molecular_functionprotein homodimerization activity
C0045995biological_processregulation of embryonic development
D0000118cellular_componenthistone deacetylase complex
D0000122biological_processnegative regulation of transcription by RNA polymerase II
D0000785cellular_componentchromatin
D0000792cellular_componentheterochromatin
D0000976molecular_functiontranscription cis-regulatory region binding
D0000978molecular_functionRNA polymerase II cis-regulatory region sequence-specific DNA binding
D0000979molecular_functionRNA polymerase II core promoter sequence-specific DNA binding
D0001046molecular_functioncore promoter sequence-specific DNA binding
D0001222molecular_functiontranscription corepressor binding
D0002039molecular_functionp53 binding
D0003677molecular_functionDNA binding
D0003682molecular_functionchromatin binding
D0003714molecular_functiontranscription corepressor activity
D0004407molecular_functionhistone deacetylase activity
D0005515molecular_functionprotein binding
D0005634cellular_componentnucleus
D0005654cellular_componentnucleoplasm
D0005667cellular_componenttranscription regulator complex
D0005737cellular_componentcytoplasm
D0005829cellular_componentcytosol
D0006325biological_processchromatin organization
D0006338biological_processchromatin remodeling
D0006346biological_processDNA methylation-dependent constitutive heterochromatin formation
D0006357biological_processregulation of transcription by RNA polymerase II
D0007623biological_processcircadian rhythm
D0008284biological_processpositive regulation of cell population proliferation
D0009913biological_processepidermal cell differentiation
D0010628biological_processpositive regulation of gene expression
D0010629biological_processnegative regulation of gene expression
D0010832biological_processnegative regulation of myotube differentiation
D0016581cellular_componentNuRD complex
D0016811molecular_functionhydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides
D0017053cellular_componenttranscription repressor complex
D0019899molecular_functionenzyme binding
D0030336biological_processnegative regulation of cell migration
D0030512biological_processnegative regulation of transforming growth factor beta receptor signaling pathway
D0031492molecular_functionnucleosomal DNA binding
D0031507biological_processheterochromatin formation
D0032922biological_processcircadian regulation of gene expression
D0032991cellular_componentprotein-containing complex
D0033148biological_processpositive regulation of intracellular estrogen receptor signaling pathway
D0033558molecular_functionprotein lysine deacetylase activity
D0035851molecular_functionKrueppel-associated box domain binding
D0036120biological_processcellular response to platelet-derived growth factor stimulus
D0042475biological_processodontogenesis of dentin-containing tooth
D0042659biological_processregulation of cell fate specification
D0042733biological_processembryonic digit morphogenesis
D0042826molecular_functionhistone deacetylase binding
D0043025cellular_componentneuronal cell body
D0043066biological_processnegative regulation of apoptotic process
D0043922biological_processhost-mediated suppression of viral transcription
D0045814biological_processnegative regulation of gene expression, epigenetic
D0045892biological_processnegative regulation of DNA-templated transcription
D0045893biological_processpositive regulation of DNA-templated transcription
D0045944biological_processpositive regulation of transcription by RNA polymerase II
D0045995biological_processregulation of embryonic development
D0048661biological_processpositive regulation of smooth muscle cell proliferation
D0051059molecular_functionNF-kappaB binding
D0060766biological_processnegative regulation of androgen receptor signaling pathway
D0060789biological_processhair follicle placode formation
D0061029biological_processeyelid development in camera-type eye
D0061198biological_processfungiform papilla formation
D0061629molecular_functionRNA polymerase II-specific DNA-binding transcription factor binding
D0070822cellular_componentSin3-type complex
D0070888molecular_functionE-box binding
D0090090biological_processnegative regulation of canonical Wnt signaling pathway
D0140297molecular_functionDNA-binding transcription factor binding
D0141221molecular_functionhistone deacetylase activity, hydrolytic mechanism
D0160008molecular_functionprotein decrotonylase activity
D0160009molecular_functionhistone decrotonylase activity
D0160216molecular_functionprotein lysine delactylase activity
D1902455biological_processnegative regulation of stem cell population maintenance
D1902459biological_processpositive regulation of stem cell population maintenance
D1990841molecular_functionpromoter-specific chromatin binding
D1990904cellular_componentribonucleoprotein complex
D2000736biological_processregulation of stem cell differentiation
F0000118cellular_componenthistone deacetylase complex
F0003677molecular_functionDNA binding
F0005515molecular_functionprotein binding
F0005634cellular_componentnucleus
F0005654cellular_componentnucleoplasm
F0005694cellular_componentchromosome
F0005730cellular_componentnucleolus
F0006325biological_processchromatin organization
F0031491molecular_functionnucleosome binding
F0042803molecular_functionprotein homodimerization activity
F0045995biological_processregulation of embryonic development
Functional Information from SwissProt/UniProt
site_idSWS_FT_FI1
Number of Residues624
DetailsRegion: {"description":"Histone deacetylase"}
ChainResidueDetails
site_idSWS_FT_FI2
Number of Residues2
DetailsActive site: {"evidences":[{"source":"PubMed","id":"19182791","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"28497810","evidenceCode":"ECO:0000269"}]}
ChainResidueDetails
site_idSWS_FT_FI3
Number of Residues12
DetailsBinding site: {"evidences":[{"source":"UniProtKB","id":"O15379","evidenceCode":"ECO:0000250"}]}
ChainResidueDetails
site_idSWS_FT_FI4
Number of Residues2
DetailsModified residue: {"description":"N6-acetyllysine; alternate","evidences":[{"source":"PubMed","id":"19608861","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails
site_idSWS_FT_FI5
Number of Residues2
DetailsModified residue: {"description":"N6-acetyllysine","evidences":[{"source":"PubMed","id":"19608861","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails
site_idSWS_FT_FI6
Number of Residues4
DetailsModified residue: {"description":"S-nitrosocysteine","evidences":[{"source":"UniProtKB","id":"P70288","evidenceCode":"ECO:0000250"}]}
ChainResidueDetails
site_idSWS_FT_FI7
Number of Residues4
DetailsCross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2); alternate","evidences":[{"source":"UniProtKB","id":"Q92769","evidenceCode":"ECO:0000250"}]}
ChainResidueDetails
site_idSWS_FT_FI8
Number of Residues184
DetailsDomain: {"description":"ELM2","evidences":[{"source":"PROSITE-ProRule","id":"PRU00512","evidenceCode":"ECO:0000255"}]}
ChainResidueDetails
site_idSWS_FT_FI9
Number of Residues2
DetailsModified residue: {"description":"Phosphothreonine","evidences":[{"source":"PubMed","id":"19690332","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails
site_idSWS_FT_FI10
Number of Residues2
DetailsModified residue: {"description":"Phosphoserine","evidences":[{"source":"PubMed","id":"19690332","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails

251801

PDB entries from 2026-04-08

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