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SummaryStructural detailsExperimental detailsFunctional detailsSequence NeighborHistoryDownloads

9GGN

Cryo-EM structure of KBTBD4 WT-HDAC2 2:2 complex mediated by molecular glue UM171

This is a non-PDB format compatible entry.
Functional Information from GO Data
ChainGOidnamespacecontents
A0043161biological_processproteasome-mediated ubiquitin-dependent protein catabolic process
B0000118cellular_componenthistone deacetylase complex
B0000122biological_processnegative regulation of transcription by RNA polymerase II
B0000781cellular_componentchromosome, telomeric region
B0000785cellular_componentchromatin
B0001221molecular_functiontranscription coregulator binding
B0001975biological_processresponse to amphetamine
B0003300biological_processcardiac muscle hypertrophy
B0003682molecular_functionchromatin binding
B0003723molecular_functionRNA binding
B0004407molecular_functionhistone deacetylase activity
B0005515molecular_functionprotein binding
B0005634cellular_componentnucleus
B0005654cellular_componentnucleoplasm
B0005737cellular_componentcytoplasm
B0006325biological_processchromatin organization
B0006338biological_processchromatin remodeling
B0006351biological_processDNA-templated transcription
B0008284biological_processpositive regulation of cell population proliferation
B0009410biological_processresponse to xenobiotic stimulus
B0009913biological_processepidermal cell differentiation
B0010718biological_processpositive regulation of epithelial to mesenchymal transition
B0010944biological_processnegative regulation of transcription by competitive promoter binding
B0010977biological_processnegative regulation of neuron projection development
B0016358biological_processdendrite development
B0016581cellular_componentNuRD complex
B0016787molecular_functionhydrolase activity
B0016811molecular_functionhydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides
B0019213molecular_functiondeacetylase activity
B0019899molecular_functionenzyme binding
B0030336biological_processnegative regulation of cell migration
B0030512biological_processnegative regulation of transforming growth factor beta receptor signaling pathway
B0031000biological_processresponse to caffeine
B0031072molecular_functionheat shock protein binding
B0031492molecular_functionnucleosomal DNA binding
B0031507biological_processheterochromatin formation
B0032496biological_processresponse to lipopolysaccharide
B0032732biological_processpositive regulation of interleukin-1 production
B0032760biological_processpositive regulation of tumor necrosis factor production
B0032922biological_processcircadian regulation of gene expression
B0032991cellular_componentprotein-containing complex
B0033148biological_processpositive regulation of intracellular estrogen receptor signaling pathway
B0033558molecular_functionprotein lysine deacetylase activity
B0034605biological_processcellular response to heat
B0035094biological_processresponse to nicotine
B0035098cellular_componentESC/E(Z) complex
B0042220biological_processresponse to cocaine
B0042393molecular_functionhistone binding
B0042475biological_processodontogenesis of dentin-containing tooth
B0042659biological_processregulation of cell fate specification
B0042733biological_processembryonic digit morphogenesis
B0042826molecular_functionhistone deacetylase binding
B0043066biological_processnegative regulation of apoptotic process
B0045862biological_processpositive regulation of proteolysis
B0045892biological_processnegative regulation of DNA-templated transcription
B0045893biological_processpositive regulation of DNA-templated transcription
B0045944biological_processpositive regulation of transcription by RNA polymerase II
B0045995biological_processregulation of embryonic development
B0048149biological_processbehavioral response to ethanol
B0048511biological_processrhythmic process
B0048714biological_processpositive regulation of oligodendrocyte differentiation
B0050847biological_processprogesterone receptor signaling pathway
B0051059molecular_functionNF-kappaB binding
B0055093biological_processresponse to hyperoxia
B0060789biological_processhair follicle placode formation
B0061000biological_processnegative regulation of dendritic spine development
B0061029biological_processeyelid development in camera-type eye
B0061198biological_processfungiform papilla formation
B0061629molecular_functionRNA polymerase II-specific DNA-binding transcription factor binding
B0070301biological_processcellular response to hydrogen peroxide
B0070822cellular_componentSin3-type complex
B0071300biological_processcellular response to retinoic acid
B0071560biological_processcellular response to transforming growth factor beta stimulus
B0097305biological_processresponse to alcohol
B0140297molecular_functionDNA-binding transcription factor binding
B0141221molecular_functionhistone deacetylase activity, hydrolytic mechanism
B0160008molecular_functionprotein decrotonylase activity
B0160009molecular_functionhistone decrotonylase activity
B0160010molecular_functionprotein de-2-hydroxyisobutyrylase activity
B0160216molecular_functionprotein lysine delactylase activity
B1902437biological_processpositive regulation of male mating behavior
B1902455biological_processnegative regulation of stem cell population maintenance
B1902459biological_processpositive regulation of stem cell population maintenance
B1903351biological_processcellular response to dopamine
B1904645biological_processresponse to amyloid-beta
B1990841molecular_functionpromoter-specific chromatin binding
B2000736biological_processregulation of stem cell differentiation
C0043161biological_processproteasome-mediated ubiquitin-dependent protein catabolic process
D0000118cellular_componenthistone deacetylase complex
D0000122biological_processnegative regulation of transcription by RNA polymerase II
D0000781cellular_componentchromosome, telomeric region
D0000785cellular_componentchromatin
D0001221molecular_functiontranscription coregulator binding
D0001975biological_processresponse to amphetamine
D0003300biological_processcardiac muscle hypertrophy
D0003682molecular_functionchromatin binding
D0003723molecular_functionRNA binding
D0004407molecular_functionhistone deacetylase activity
D0005515molecular_functionprotein binding
D0005634cellular_componentnucleus
D0005654cellular_componentnucleoplasm
D0005737cellular_componentcytoplasm
D0006325biological_processchromatin organization
D0006338biological_processchromatin remodeling
D0006351biological_processDNA-templated transcription
D0008284biological_processpositive regulation of cell population proliferation
D0009410biological_processresponse to xenobiotic stimulus
D0009913biological_processepidermal cell differentiation
D0010718biological_processpositive regulation of epithelial to mesenchymal transition
D0010944biological_processnegative regulation of transcription by competitive promoter binding
D0010977biological_processnegative regulation of neuron projection development
D0016358biological_processdendrite development
D0016581cellular_componentNuRD complex
D0016787molecular_functionhydrolase activity
D0016811molecular_functionhydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides
D0019213molecular_functiondeacetylase activity
D0019899molecular_functionenzyme binding
D0030336biological_processnegative regulation of cell migration
D0030512biological_processnegative regulation of transforming growth factor beta receptor signaling pathway
D0031000biological_processresponse to caffeine
D0031072molecular_functionheat shock protein binding
D0031492molecular_functionnucleosomal DNA binding
D0031507biological_processheterochromatin formation
D0032496biological_processresponse to lipopolysaccharide
D0032732biological_processpositive regulation of interleukin-1 production
D0032760biological_processpositive regulation of tumor necrosis factor production
D0032922biological_processcircadian regulation of gene expression
D0032991cellular_componentprotein-containing complex
D0033148biological_processpositive regulation of intracellular estrogen receptor signaling pathway
D0033558molecular_functionprotein lysine deacetylase activity
D0034605biological_processcellular response to heat
D0035094biological_processresponse to nicotine
D0035098cellular_componentESC/E(Z) complex
D0042220biological_processresponse to cocaine
D0042393molecular_functionhistone binding
D0042475biological_processodontogenesis of dentin-containing tooth
D0042659biological_processregulation of cell fate specification
D0042733biological_processembryonic digit morphogenesis
D0042826molecular_functionhistone deacetylase binding
D0043066biological_processnegative regulation of apoptotic process
D0045862biological_processpositive regulation of proteolysis
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
D0048149biological_processbehavioral response to ethanol
D0048511biological_processrhythmic process
D0048714biological_processpositive regulation of oligodendrocyte differentiation
D0050847biological_processprogesterone receptor signaling pathway
D0051059molecular_functionNF-kappaB binding
D0055093biological_processresponse to hyperoxia
D0060789biological_processhair follicle placode formation
D0061000biological_processnegative regulation of dendritic spine development
D0061029biological_processeyelid development in camera-type eye
D0061198biological_processfungiform papilla formation
D0061629molecular_functionRNA polymerase II-specific DNA-binding transcription factor binding
D0070301biological_processcellular response to hydrogen peroxide
D0070822cellular_componentSin3-type complex
D0071300biological_processcellular response to retinoic acid
D0071560biological_processcellular response to transforming growth factor beta stimulus
D0097305biological_processresponse to alcohol
D0140297molecular_functionDNA-binding transcription factor binding
D0141221molecular_functionhistone deacetylase activity, hydrolytic mechanism
D0160008molecular_functionprotein decrotonylase activity
D0160009molecular_functionhistone decrotonylase activity
D0160010molecular_functionprotein de-2-hydroxyisobutyrylase activity
D0160216molecular_functionprotein lysine delactylase activity
D1902437biological_processpositive regulation of male mating behavior
D1902455biological_processnegative regulation of stem cell population maintenance
D1902459biological_processpositive regulation of stem cell population maintenance
D1903351biological_processcellular response to dopamine
D1904645biological_processresponse to amyloid-beta
D1990841molecular_functionpromoter-specific chromatin binding
D2000736biological_processregulation of stem cell differentiation
Functional Information from SwissProt/UniProt
site_idSWS_FT_FI1
Number of Residues94
DetailsRepeat: {"description":"Kelch 3","evidences":[{"evidenceCode":"ECO:0000255"}]}
ChainResidueDetails
site_idSWS_FT_FI2
Number of Residues100
DetailsRepeat: {"description":"Kelch 4","evidences":[{"evidenceCode":"ECO:0000255"}]}
ChainResidueDetails
site_idSWS_FT_FI3
Number of Residues2
DetailsActive site: {"evidences":[{"source":"UniProtKB","id":"Q13547","evidenceCode":"ECO:0000250"}]}
ChainResidueDetails
site_idSWS_FT_FI4
Number of Residues6
DetailsBinding site: {"evidences":[{"source":"UniProtKB","id":"O15379","evidenceCode":"ECO:0000250"}]}
ChainResidueDetails
site_idSWS_FT_FI5
Number of Residues18
DetailsBinding site: {"evidences":[{"source":"PubMed","id":"37137925","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"8BPA","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"8BPB","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"8BPC","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails
site_idSWS_FT_FI6
Number of Residues2
DetailsBinding site: {"evidences":[{"source":"PubMed","id":"37137925","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"8BPB","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"8BPC","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails
site_idSWS_FT_FI7
Number of Residues2
DetailsModified residue: {"description":"N6-acetyllysine; alternate","evidences":[{"source":"UniProtKB","id":"Q13547","evidenceCode":"ECO:0000250"}]}
ChainResidueDetails
site_idSWS_FT_FI8
Number of Residues2
DetailsModified residue: {"description":"N6-acetyllysine","evidences":[{"source":"UniProtKB","id":"Q13547","evidenceCode":"ECO:0000250"}]}
ChainResidueDetails
site_idSWS_FT_FI9
Number of Residues4
DetailsModified residue: {"description":"S-nitrosocysteine","evidences":[{"source":"UniProtKB","id":"P70288","evidenceCode":"ECO:0000250"}]}
ChainResidueDetails
site_idSWS_FT_FI10
Number of Residues4
DetailsCross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2); alternate","evidences":[{"source":"PubMed","id":"28112733","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails

247536

PDB entries from 2026-01-14

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