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6Z2K

The structure of the tetrameric HDAC1/MIDEAS/DNTTIP1 MiDAC deacetylase complex

Functional Information from GO Data
ChainGOidnamespacecontents
C0000118cellular_componenthistone deacetylase complex
C0000122biological_processnegative regulation of transcription by RNA polymerase II
C0000785cellular_componentchromatin
C0000792cellular_componentheterochromatin
C0000976molecular_functiontranscription cis-regulatory region binding
C0000978molecular_functionRNA polymerase II cis-regulatory region sequence-specific DNA binding
C0000979molecular_functionRNA polymerase II core promoter sequence-specific DNA binding
C0001046molecular_functioncore promoter sequence-specific DNA binding
C0001222molecular_functiontranscription corepressor binding
C0002039molecular_functionp53 binding
C0003677molecular_functionDNA binding
C0003682molecular_functionchromatin binding
C0003714molecular_functiontranscription corepressor activity
C0004407molecular_functionhistone deacetylase activity
C0005515molecular_functionprotein binding
C0005634cellular_componentnucleus
C0005654cellular_componentnucleoplasm
C0005667cellular_componenttranscription regulator complex
C0005737cellular_componentcytoplasm
C0005829cellular_componentcytosol
C0006325biological_processchromatin organization
C0006338biological_processchromatin remodeling
C0006346biological_processDNA methylation-dependent constitutive heterochromatin formation
C0006357biological_processregulation of transcription by RNA polymerase II
C0006476biological_processprotein deacetylation
C0007492biological_processendoderm development
C0007623biological_processcircadian rhythm
C0008284biological_processpositive regulation of cell population proliferation
C0009913biological_processepidermal cell differentiation
C0010628biological_processpositive regulation of gene expression
C0010629biological_processnegative regulation of gene expression
C0010832biological_processnegative regulation of myotube differentiation
C0016581cellular_componentNuRD complex
C0016787molecular_functionhydrolase activity
C0016811molecular_functionhydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides
C0017053cellular_componenttranscription repressor complex
C0019899molecular_functionenzyme binding
C0021766biological_processhippocampus development
C0030182biological_processneuron differentiation
C0030336biological_processnegative regulation of cell migration
C0030512biological_processnegative regulation of transforming growth factor beta receptor signaling pathway
C0031492molecular_functionnucleosomal DNA binding
C0031507biological_processheterochromatin formation
C0032922biological_processcircadian regulation of gene expression
C0032991cellular_componentprotein-containing complex
C0033148biological_processpositive regulation of intracellular estrogen receptor signaling pathway
C0033558molecular_functionprotein lysine deacetylase activity
C0035851molecular_functionKrueppel-associated box domain binding
C0036120biological_processcellular response to platelet-derived growth factor stimulus
C0042475biological_processodontogenesis of dentin-containing tooth
C0042659biological_processregulation of cell fate specification
C0042733biological_processembryonic digit morphogenesis
C0042826molecular_functionhistone deacetylase binding
C0043025cellular_componentneuronal cell body
C0043066biological_processnegative regulation of apoptotic process
C0043124biological_processnegative regulation of canonical NF-kappaB signal transduction
C0043922biological_processnegative regulation by host of viral transcription
C0045814biological_processnegative regulation of gene expression, epigenetic
C0045892biological_processnegative regulation of DNA-templated transcription
C0045893biological_processpositive regulation of DNA-templated transcription
C0045944biological_processpositive regulation of transcription by RNA polymerase II
C0046872molecular_functionmetal ion binding
C0048511biological_processrhythmic process
C0048661biological_processpositive regulation of smooth muscle cell proliferation
C0048709biological_processoligodendrocyte differentiation
C0048714biological_processpositive regulation of oligodendrocyte differentiation
C0051059molecular_functionNF-kappaB binding
C0060766biological_processnegative regulation of androgen receptor signaling pathway
C0060789biological_processhair follicle placode formation
C0061029biological_processeyelid development in camera-type eye
C0061198biological_processfungiform papilla formation
C0061629molecular_functionRNA polymerase II-specific DNA-binding transcription factor binding
C0070822cellular_componentSin3-type complex
C0070888molecular_functionE-box binding
C0090090biological_processnegative regulation of canonical Wnt signaling pathway
C0140297molecular_functionDNA-binding transcription factor binding
C0141221molecular_functionhistone deacetylase activity, hydrolytic mechanism
C0160008molecular_functionprotein decrotonylase activity
C0160009molecular_functionhistone decrotonylase activity
C0160216molecular_functionprotein lysine delactylase activity
C1902455biological_processnegative regulation of stem cell population maintenance
C1902459biological_processpositive regulation of stem cell population maintenance
C1990841molecular_functionpromoter-specific chromatin binding
C2000736biological_processregulation of stem cell differentiation
C2001243biological_processnegative regulation of intrinsic apoptotic signaling pathway
E0000118cellular_componenthistone deacetylase complex
E0000122biological_processnegative regulation of transcription by RNA polymerase II
E0000785cellular_componentchromatin
E0000792cellular_componentheterochromatin
E0000976molecular_functiontranscription cis-regulatory region binding
E0000978molecular_functionRNA polymerase II cis-regulatory region sequence-specific DNA binding
E0000979molecular_functionRNA polymerase II core promoter sequence-specific DNA binding
E0001046molecular_functioncore promoter sequence-specific DNA binding
E0001222molecular_functiontranscription corepressor binding
E0002039molecular_functionp53 binding
E0003677molecular_functionDNA binding
E0003682molecular_functionchromatin binding
E0003714molecular_functiontranscription corepressor activity
E0004407molecular_functionhistone deacetylase activity
E0005515molecular_functionprotein binding
E0005634cellular_componentnucleus
E0005654cellular_componentnucleoplasm
E0005667cellular_componenttranscription regulator complex
E0005737cellular_componentcytoplasm
E0005829cellular_componentcytosol
E0006325biological_processchromatin organization
E0006338biological_processchromatin remodeling
E0006346biological_processDNA methylation-dependent constitutive heterochromatin formation
E0006357biological_processregulation of transcription by RNA polymerase II
E0006476biological_processprotein deacetylation
E0007492biological_processendoderm development
E0007623biological_processcircadian rhythm
E0008284biological_processpositive regulation of cell population proliferation
E0009913biological_processepidermal cell differentiation
E0010628biological_processpositive regulation of gene expression
E0010629biological_processnegative regulation of gene expression
E0010832biological_processnegative regulation of myotube differentiation
E0016581cellular_componentNuRD complex
E0016787molecular_functionhydrolase activity
E0016811molecular_functionhydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides
E0017053cellular_componenttranscription repressor complex
E0019899molecular_functionenzyme binding
E0021766biological_processhippocampus development
E0030182biological_processneuron differentiation
E0030336biological_processnegative regulation of cell migration
E0030512biological_processnegative regulation of transforming growth factor beta receptor signaling pathway
E0031492molecular_functionnucleosomal DNA binding
E0031507biological_processheterochromatin formation
E0032922biological_processcircadian regulation of gene expression
E0032991cellular_componentprotein-containing complex
E0033148biological_processpositive regulation of intracellular estrogen receptor signaling pathway
E0033558molecular_functionprotein lysine deacetylase activity
E0035851molecular_functionKrueppel-associated box domain binding
E0036120biological_processcellular response to platelet-derived growth factor stimulus
E0042475biological_processodontogenesis of dentin-containing tooth
E0042659biological_processregulation of cell fate specification
E0042733biological_processembryonic digit morphogenesis
E0042826molecular_functionhistone deacetylase binding
E0043025cellular_componentneuronal cell body
E0043066biological_processnegative regulation of apoptotic process
E0043124biological_processnegative regulation of canonical NF-kappaB signal transduction
E0043922biological_processnegative regulation by host of viral transcription
E0045814biological_processnegative regulation of gene expression, epigenetic
E0045892biological_processnegative regulation of DNA-templated transcription
E0045893biological_processpositive regulation of DNA-templated transcription
E0045944biological_processpositive regulation of transcription by RNA polymerase II
E0046872molecular_functionmetal ion binding
E0048511biological_processrhythmic process
E0048661biological_processpositive regulation of smooth muscle cell proliferation
E0048709biological_processoligodendrocyte differentiation
E0048714biological_processpositive regulation of oligodendrocyte differentiation
E0051059molecular_functionNF-kappaB binding
E0060766biological_processnegative regulation of androgen receptor signaling pathway
E0060789biological_processhair follicle placode formation
E0061029biological_processeyelid development in camera-type eye
E0061198biological_processfungiform papilla formation
E0061629molecular_functionRNA polymerase II-specific DNA-binding transcription factor binding
E0070822cellular_componentSin3-type complex
E0070888molecular_functionE-box binding
E0090090biological_processnegative regulation of canonical Wnt signaling pathway
E0140297molecular_functionDNA-binding transcription factor binding
E0141221molecular_functionhistone deacetylase activity, hydrolytic mechanism
E0160008molecular_functionprotein decrotonylase activity
E0160009molecular_functionhistone decrotonylase activity
E0160216molecular_functionprotein lysine delactylase activity
E1902455biological_processnegative regulation of stem cell population maintenance
E1902459biological_processpositive regulation of stem cell population maintenance
E1990841molecular_functionpromoter-specific chromatin binding
E2000736biological_processregulation of stem cell differentiation
E2001243biological_processnegative regulation of intrinsic apoptotic signaling pathway
I0000118cellular_componenthistone deacetylase complex
I0000122biological_processnegative regulation of transcription by RNA polymerase II
I0000785cellular_componentchromatin
I0000792cellular_componentheterochromatin
I0000976molecular_functiontranscription cis-regulatory region binding
I0000978molecular_functionRNA polymerase II cis-regulatory region sequence-specific DNA binding
I0000979molecular_functionRNA polymerase II core promoter sequence-specific DNA binding
I0001046molecular_functioncore promoter sequence-specific DNA binding
I0001222molecular_functiontranscription corepressor binding
I0002039molecular_functionp53 binding
I0003677molecular_functionDNA binding
I0003682molecular_functionchromatin binding
I0003714molecular_functiontranscription corepressor activity
I0004407molecular_functionhistone deacetylase activity
I0005515molecular_functionprotein binding
I0005634cellular_componentnucleus
I0005654cellular_componentnucleoplasm
I0005667cellular_componenttranscription regulator complex
I0005737cellular_componentcytoplasm
I0005829cellular_componentcytosol
I0006325biological_processchromatin organization
I0006338biological_processchromatin remodeling
I0006346biological_processDNA methylation-dependent constitutive heterochromatin formation
I0006357biological_processregulation of transcription by RNA polymerase II
I0006476biological_processprotein deacetylation
I0007492biological_processendoderm development
I0007623biological_processcircadian rhythm
I0008284biological_processpositive regulation of cell population proliferation
I0009913biological_processepidermal cell differentiation
I0010628biological_processpositive regulation of gene expression
I0010629biological_processnegative regulation of gene expression
I0010832biological_processnegative regulation of myotube differentiation
I0016581cellular_componentNuRD complex
I0016787molecular_functionhydrolase activity
I0016811molecular_functionhydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides
I0017053cellular_componenttranscription repressor complex
I0019899molecular_functionenzyme binding
I0021766biological_processhippocampus development
I0030182biological_processneuron differentiation
I0030336biological_processnegative regulation of cell migration
I0030512biological_processnegative regulation of transforming growth factor beta receptor signaling pathway
I0031492molecular_functionnucleosomal DNA binding
I0031507biological_processheterochromatin formation
I0032922biological_processcircadian regulation of gene expression
I0032991cellular_componentprotein-containing complex
I0033148biological_processpositive regulation of intracellular estrogen receptor signaling pathway
I0033558molecular_functionprotein lysine deacetylase activity
I0035851molecular_functionKrueppel-associated box domain binding
I0036120biological_processcellular response to platelet-derived growth factor stimulus
I0042475biological_processodontogenesis of dentin-containing tooth
I0042659biological_processregulation of cell fate specification
I0042733biological_processembryonic digit morphogenesis
I0042826molecular_functionhistone deacetylase binding
I0043025cellular_componentneuronal cell body
I0043066biological_processnegative regulation of apoptotic process
I0043124biological_processnegative regulation of canonical NF-kappaB signal transduction
I0043922biological_processnegative regulation by host of viral transcription
I0045814biological_processnegative regulation of gene expression, epigenetic
I0045892biological_processnegative regulation of DNA-templated transcription
I0045893biological_processpositive regulation of DNA-templated transcription
I0045944biological_processpositive regulation of transcription by RNA polymerase II
I0046872molecular_functionmetal ion binding
I0048511biological_processrhythmic process
I0048661biological_processpositive regulation of smooth muscle cell proliferation
I0048709biological_processoligodendrocyte differentiation
I0048714biological_processpositive regulation of oligodendrocyte differentiation
I0051059molecular_functionNF-kappaB binding
I0060766biological_processnegative regulation of androgen receptor signaling pathway
I0060789biological_processhair follicle placode formation
I0061029biological_processeyelid development in camera-type eye
I0061198biological_processfungiform papilla formation
I0061629molecular_functionRNA polymerase II-specific DNA-binding transcription factor binding
I0070822cellular_componentSin3-type complex
I0070888molecular_functionE-box binding
I0090090biological_processnegative regulation of canonical Wnt signaling pathway
I0140297molecular_functionDNA-binding transcription factor binding
I0141221molecular_functionhistone deacetylase activity, hydrolytic mechanism
I0160008molecular_functionprotein decrotonylase activity
I0160009molecular_functionhistone decrotonylase activity
I0160216molecular_functionprotein lysine delactylase activity
I1902455biological_processnegative regulation of stem cell population maintenance
I1902459biological_processpositive regulation of stem cell population maintenance
I1990841molecular_functionpromoter-specific chromatin binding
I2000736biological_processregulation of stem cell differentiation
I2001243biological_processnegative regulation of intrinsic apoptotic signaling pathway
K0000118cellular_componenthistone deacetylase complex
K0000122biological_processnegative regulation of transcription by RNA polymerase II
K0000785cellular_componentchromatin
K0000792cellular_componentheterochromatin
K0000976molecular_functiontranscription cis-regulatory region binding
K0000978molecular_functionRNA polymerase II cis-regulatory region sequence-specific DNA binding
K0000979molecular_functionRNA polymerase II core promoter sequence-specific DNA binding
K0001046molecular_functioncore promoter sequence-specific DNA binding
K0001222molecular_functiontranscription corepressor binding
K0002039molecular_functionp53 binding
K0003677molecular_functionDNA binding
K0003682molecular_functionchromatin binding
K0003714molecular_functiontranscription corepressor activity
K0004407molecular_functionhistone deacetylase activity
K0005515molecular_functionprotein binding
K0005634cellular_componentnucleus
K0005654cellular_componentnucleoplasm
K0005667cellular_componenttranscription regulator complex
K0005737cellular_componentcytoplasm
K0005829cellular_componentcytosol
K0006325biological_processchromatin organization
K0006338biological_processchromatin remodeling
K0006346biological_processDNA methylation-dependent constitutive heterochromatin formation
K0006357biological_processregulation of transcription by RNA polymerase II
K0006476biological_processprotein deacetylation
K0007492biological_processendoderm development
K0007623biological_processcircadian rhythm
K0008284biological_processpositive regulation of cell population proliferation
K0009913biological_processepidermal cell differentiation
K0010628biological_processpositive regulation of gene expression
K0010629biological_processnegative regulation of gene expression
K0010832biological_processnegative regulation of myotube differentiation
K0016581cellular_componentNuRD complex
K0016787molecular_functionhydrolase activity
K0016811molecular_functionhydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides
K0017053cellular_componenttranscription repressor complex
K0019899molecular_functionenzyme binding
K0021766biological_processhippocampus development
K0030182biological_processneuron differentiation
K0030336biological_processnegative regulation of cell migration
K0030512biological_processnegative regulation of transforming growth factor beta receptor signaling pathway
K0031492molecular_functionnucleosomal DNA binding
K0031507biological_processheterochromatin formation
K0032922biological_processcircadian regulation of gene expression
K0032991cellular_componentprotein-containing complex
K0033148biological_processpositive regulation of intracellular estrogen receptor signaling pathway
K0033558molecular_functionprotein lysine deacetylase activity
K0035851molecular_functionKrueppel-associated box domain binding
K0036120biological_processcellular response to platelet-derived growth factor stimulus
K0042475biological_processodontogenesis of dentin-containing tooth
K0042659biological_processregulation of cell fate specification
K0042733biological_processembryonic digit morphogenesis
K0042826molecular_functionhistone deacetylase binding
K0043025cellular_componentneuronal cell body
K0043066biological_processnegative regulation of apoptotic process
K0043124biological_processnegative regulation of canonical NF-kappaB signal transduction
K0043922biological_processnegative regulation by host of viral transcription
K0045814biological_processnegative regulation of gene expression, epigenetic
K0045892biological_processnegative regulation of DNA-templated transcription
K0045893biological_processpositive regulation of DNA-templated transcription
K0045944biological_processpositive regulation of transcription by RNA polymerase II
K0046872molecular_functionmetal ion binding
K0048511biological_processrhythmic process
K0048661biological_processpositive regulation of smooth muscle cell proliferation
K0048709biological_processoligodendrocyte differentiation
K0048714biological_processpositive regulation of oligodendrocyte differentiation
K0051059molecular_functionNF-kappaB binding
K0060766biological_processnegative regulation of androgen receptor signaling pathway
K0060789biological_processhair follicle placode formation
K0061029biological_processeyelid development in camera-type eye
K0061198biological_processfungiform papilla formation
K0061629molecular_functionRNA polymerase II-specific DNA-binding transcription factor binding
K0070822cellular_componentSin3-type complex
K0070888molecular_functionE-box binding
K0090090biological_processnegative regulation of canonical Wnt signaling pathway
K0140297molecular_functionDNA-binding transcription factor binding
K0141221molecular_functionhistone deacetylase activity, hydrolytic mechanism
K0160008molecular_functionprotein decrotonylase activity
K0160009molecular_functionhistone decrotonylase activity
K0160216molecular_functionprotein lysine delactylase activity
K1902455biological_processnegative regulation of stem cell population maintenance
K1902459biological_processpositive regulation of stem cell population maintenance
K1990841molecular_functionpromoter-specific chromatin binding
K2000736biological_processregulation of stem cell differentiation
K2001243biological_processnegative regulation of intrinsic apoptotic signaling pathway
Functional Information from PDB Data
site_idAC1
Number of Residues3
Detailsbinding site for residue ZN C 501
ChainResidue
CASP176
CHIS178
CASP264

site_idAC2
Number of Residues5
Detailsbinding site for residue K C 502
ChainResidue
CASP174
CASP176
CHIS178
CSER197
CPHE198

site_idAC3
Number of Residues4
Detailsbinding site for residue K C 503
ChainResidue
CTHR190
CVAL193
CTYR222
CPHE187

site_idAC4
Number of Residues4
Detailsbinding site for residue IHP E 501
ChainResidue
EGLY27
ELYS31
FLYS875
LLYS839

site_idAC5
Number of Residues3
Detailsbinding site for residue ZN E 502
ChainResidue
EASP176
EHIS178
EASP264

site_idAC6
Number of Residues5
Detailsbinding site for residue K E 503
ChainResidue
EASP174
EASP176
EHIS178
ESER197
EPHE198

site_idAC7
Number of Residues4
Detailsbinding site for residue K E 504
ChainResidue
EPHE187
ETHR190
EVAL193
ETYR222

site_idAC8
Number of Residues3
Detailsbinding site for residue ZN K 501
ChainResidue
KASP176
KHIS178
KASP264

site_idAC9
Number of Residues5
Detailsbinding site for residue K K 502
ChainResidue
KASP174
KASP176
KHIS178
KSER197
KPHE198

site_idAD1
Number of Residues4
Detailsbinding site for residue K K 503
ChainResidue
KPHE187
KTHR190
KVAL193
KTYR222

site_idAD2
Number of Residues3
Detailsbinding site for residue ZN I 501
ChainResidue
IASP176
IHIS178
IASP264

site_idAD3
Number of Residues5
Detailsbinding site for residue K I 502
ChainResidue
IASP174
IASP176
IHIS178
ISER197
IPHE198

site_idAD4
Number of Residues4
Detailsbinding site for residue K I 503
ChainResidue
IPHE187
ITHR190
IVAL193
ITYR222

site_idAD5
Number of Residues5
Detailsbinding site for residue IHP F 901
ChainResidue
FLYS839
FLYS843
KARG270
LTYR871
LLYS875

site_idAD6
Number of Residues5
Detailsbinding site for residue IHP D 901
ChainResidue
DLYS839
DLYS843
IGLY27
ILYS31
JLYS875

site_idAD7
Number of Residues4
Detailsbinding site for residue IHP J 901
ChainResidue
CGLY27
DTYR871
JLYS839
JLYS843

Functional Information from SwissProt/UniProt
site_idSWS_FT_FI1
Number of Residues1248
DetailsRegion: {"description":"Histone deacetylase"}
ChainResidueDetails

site_idSWS_FT_FI2
Number of Residues4
DetailsActive site: {"evidences":[{"source":"PubMed","id":"19182791","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"28497810","evidenceCode":"ECO:0000269"}]}
ChainResidueDetails

site_idSWS_FT_FI3
Number of Residues24
DetailsBinding site: {"evidences":[{"source":"UniProtKB","id":"O15379","evidenceCode":"ECO:0000250"}]}
ChainResidueDetails

site_idSWS_FT_FI4
Number of Residues4
DetailsModified residue: {"description":"N6-acetyllysine; alternate","evidences":[{"source":"PubMed","id":"19608861","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails

site_idSWS_FT_FI5
Number of Residues4
DetailsModified residue: {"description":"N6-acetyllysine","evidences":[{"source":"PubMed","id":"19608861","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails

site_idSWS_FT_FI6
Number of Residues8
DetailsModified residue: {"description":"S-nitrosocysteine","evidences":[{"source":"UniProtKB","id":"P70288","evidenceCode":"ECO:0000250"}]}
ChainResidueDetails

site_idSWS_FT_FI7
Number of Residues8
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 Residues368
DetailsDomain: {"description":"ELM2","evidences":[{"source":"PROSITE-ProRule","id":"PRU00512","evidenceCode":"ECO:0000255"}]}
ChainResidueDetails

238582

PDB entries from 2025-07-09

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