5zoo

Crystal structure of histone deacetylase 4 (HDAC4) in complex with a SMRT corepressor SP1 fragment

Method: X-RAY DIFFRACTION D_max: 72.9 Å Quality: GOOD

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Histone deacetylase 4

Homo sapiens

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain G； UniProt 652–1053	Fragment：UNP residues 652-1052 Mutation：H976Y	SMRT corepressor SP1 fragment × 1 K POTASSIUM ION × 2 ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions：EVAPORATION；pH 7.5；295 K；PEG 3350, iso-propanol	Resolution 1.85 Å R-free 0.175

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 5ZOO	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2H8N Structure of a glutamine-rich domain from histone deacetylase 4 Deposited 2006-06-07	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 62–153（92 aa） Fragment：N-terminal glutamine-rich Domain, residues 62-129 Chain B 62–153（92 aa） Fragment：N-terminal glutamine-rich Domain, residues 62-129 Chain C 62–153（92 aa） Fragment：N-terminal glutamine-rich Domain, residues 62-129 Chain D 62–153（92 aa） Fragment：N-terminal glutamine-rich Domain, residues 62-129	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；291 K；0.825M LITHIUM SULFATE, 55mM HEPES PH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K, pH 7.50	Resolution 2.60 Å R-free 0.307
2O94 The 97H/F mutant Structure of a glutamine-rich domain from histone deacetylase 4 Deposited 2006-12-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 62–153（92 aa） Fragment：N-terminal glutamine-rich domain, residues 62-129 Chain B 62–153（92 aa） Fragment：N-terminal glutamine-rich domain, residues 62-129 Chain C 62–153（92 aa） Fragment：N-terminal glutamine-rich domain, residues 62-129 Chain D 62–153（92 aa） Fragment：N-terminal glutamine-rich domain, residues 62-129	Mutation：H97F Mutation：H97F Mutation：H97F Mutation：H97F	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；0.540M LITHIUM SULFATE 55mM HEPES PH7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 3.00 Å R-free 0.327
2VQJ Structure of HDAC4 catalytic domain bound to a trifluoromethylketone inhbitor Deposited 2008-03-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 648–1057（410 aa） Fragment：CATALYTIC DOMAIN, RESIDUES 648-1057	Not recorded	DIO 1,4-DIETHYLENE DIOXIDE × 1 K POTASSIUM ION × 2 SO4 SULFATE ION × 3 TFG 2,2,2-TRIFLUORO-1-{5-[(3-PHENYL-5,6-DIHYDROIMIDAZO[1,2-A]PYRAZIN-7(8H)-YL)CARBONYL]THIOPHEN-2-YL}ETHANE-1,1-DIOL × 1 ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；1.6M AMMONIUM SULPHATE, 0.1M MES PH 6.5, 10% DIOXANE 1MM DTT	Resolution 2.10 Å R-free 0.276
2VQM Structure of HDAC4 catalytic domain bound to a hydroxamic acid inhbitor Deposited 2008-03-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 648–1057（410 aa） Fragment：CATALYTIC DOMAIN, RESIDUES 648-1057	Not recorded	K POTASSIUM ION × 2 HA3 N-hydroxy-5-[(3-phenyl-5,6-dihydroimidazo[1,2-a]pyrazin-7(8H)-yl)carbonyl]thiophene-2-carboxamide × 1 ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.4；1.5M AMMONIUM SULPHATE 0.1M MES PH 6.4 10% DIOXANE 1MM DTT	Resolution 1.80 Å R-free 0.256
2VQO Structure of HDAC4 catalytic domain with a gain-of-function muation bound to a trifluoromethylketone inhbitor Deposited 2008-03-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 648–1057（410 aa） Fragment：CATALYTIC DOMAIN, RESIDUES 648-1057	Mutation：YES	SO4 SULFATE ION × 2 K POTASSIUM ION × 2 TFG 2,2,2-TRIFLUORO-1-{5-[(3-PHENYL-5,6-DIHYDROIMIDAZO[1,2-A]PYRAZIN-7(8H)-YL)CARBONYL]THIOPHEN-2-YL}ETHANE-1,1-DIOL × 1 ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；1.6M AMMONIUM SULPHATE, 0.1M MES PH 6.5, 10% DIOXANE, 1MM DTT	Resolution 2.15 Å R-free 0.250
2VQO Structure of HDAC4 catalytic domain with a gain-of-function muation bound to a trifluoromethylketone inhbitor Deposited 2008-03-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 648–1057（410 aa） Fragment：CATALYTIC DOMAIN, RESIDUES 648-1057	Mutation：YES	SO4 SULFATE ION × 1 K POTASSIUM ION × 2 TFG 2,2,2-TRIFLUORO-1-{5-[(3-PHENYL-5,6-DIHYDROIMIDAZO[1,2-A]PYRAZIN-7(8H)-YL)CARBONYL]THIOPHEN-2-YL}ETHANE-1,1-DIOL × 1 ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；1.6M AMMONIUM SULPHATE, 0.1M MES PH 6.5, 10% DIOXANE, 1MM DTT	Resolution 2.15 Å R-free 0.250
2VQQ Structure of HDAC4 catalytic domain (a double cysteine-to-alanine mutant) bound to a trifluoromethylketone inhbitor Deposited 2008-03-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 648–1057（410 aa） Fragment：CATALYTIC DOMAIN, RESIDUES 648-1057	Mutation：YES	SO4 SULFATE ION × 2 K POTASSIUM ION × 2 TFG 2,2,2-TRIFLUORO-1-{5-[(3-PHENYL-5,6-DIHYDROIMIDAZO[1,2-A]PYRAZIN-7(8H)-YL)CARBONYL]THIOPHEN-2-YL}ETHANE-1,1-DIOL × 1 ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；1.6M AMMONIUM SULPHATE, 0.1M MES PH 6.5, 10% DIOXANE 1MM DTT	Resolution 1.90 Å R-free 0.221
2VQQ Structure of HDAC4 catalytic domain (a double cysteine-to-alanine mutant) bound to a trifluoromethylketone inhbitor Deposited 2008-03-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 648–1057（410 aa） Fragment：CATALYTIC DOMAIN, RESIDUES 648-1057	Mutation：YES	SO4 SULFATE ION × 1 K POTASSIUM ION × 2 TFG 2,2,2-TRIFLUORO-1-{5-[(3-PHENYL-5,6-DIHYDROIMIDAZO[1,2-A]PYRAZIN-7(8H)-YL)CARBONYL]THIOPHEN-2-YL}ETHANE-1,1-DIOL × 1 ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；1.6M AMMONIUM SULPHATE, 0.1M MES PH 6.5, 10% DIOXANE 1MM DTT	Resolution 1.90 Å R-free 0.221
2VQV Structure of HDAC4 catalytic domain with a gain-of-function mutation bound to a hydroxamic acid inhibitor Deposited 2008-03-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 648–1057（410 aa） Fragment：CATALYTIC DOMAIN, RESIDUES 648-1057	Mutation：YES	SO4 SULFATE ION × 1 K POTASSIUM ION × 2 HA3 N-hydroxy-5-[(3-phenyl-5,6-dihydroimidazo[1,2-a]pyrazin-7(8H)-yl)carbonyl]thiophene-2-carboxamide × 1 ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；0.1M MES PH 6.5, 1.6M AMMONIUM SULPHATE, 10% DIOXANE 1MM DTT	Resolution 3.30 Å R-free 0.265
2VQV Structure of HDAC4 catalytic domain with a gain-of-function mutation bound to a hydroxamic acid inhibitor Deposited 2008-03-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 648–1057（410 aa） Fragment：CATALYTIC DOMAIN, RESIDUES 648-1057	Mutation：YES	SO4 SULFATE ION × 3 K POTASSIUM ION × 2 HA3 N-hydroxy-5-[(3-phenyl-5,6-dihydroimidazo[1,2-a]pyrazin-7(8H)-yl)carbonyl]thiophene-2-carboxamide × 1 ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；0.1M MES PH 6.5, 1.6M AMMONIUM SULPHATE, 10% DIOXANE 1MM DTT	Resolution 3.30 Å R-free 0.265
2VQW Structure of inhibitor-free HDAC4 catalytic domain (with gain-of- function mutation His332Tyr) Deposited 2008-03-19	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain G 648–1057（410 aa） Fragment：CATALYTIC DOMAIN, RESIDUES 648-1057	Mutation：YES	K POTASSIUM ION × 2 ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；0.1M HEPES PH 7.5, 18% PEG 10000, 1MM DTT	Resolution 3.00 Å R-free 0.261
3UXG Crystal structure of RFXANK Deposited 2011-12-05	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 343–359（17 aa）	Not recorded	UNX UNKNOWN LIGAND × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；291 K；25% PEG3350, 0.2M sodium chloride, 0.1M HEPES, pH 7.5, vapor diffusion, sitting drop, temperature 291K	Resolution 1.85 Å R-free 0.222
3UXG Crystal structure of RFXANK Deposited 2011-12-05	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 343–359（17 aa）	Not recorded	UNX UNKNOWN LIGAND × 10	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；291 K；25% PEG3350, 0.2M sodium chloride, 0.1M HEPES, pH 7.5, vapor diffusion, sitting drop, temperature 291K	Resolution 1.85 Å R-free 0.222
3UZD Crystal structure of 14-3-3 GAMMA Deposited 2011-12-07	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain B 343–359（17 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	NO3 NITRATE ION × 12 MG MAGNESIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；0.3M Mg (OAc)2, 20% PEG3350, vapor diffusion, hanging drop, temperature 291K	Resolution 1.86 Å R-free 0.230
3UZD Crystal structure of 14-3-3 GAMMA Deposited 2011-12-07	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 343–359（17 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	NO3 NITRATE ION × 6 MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；0.3M Mg (OAc)2, 20% PEG3350, vapor diffusion, hanging drop, temperature 291K	Resolution 1.86 Å R-free 0.230
3UZD Crystal structure of 14-3-3 GAMMA Deposited 2011-12-07	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 343–359（17 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	NO3 NITRATE ION × 3 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；0.3M Mg (OAc)2, 20% PEG3350, vapor diffusion, hanging drop, temperature 291K	Resolution 1.86 Å R-free 0.230
3V31 Crystal Structure of the Peptide Bound Complex of the Ankyrin Repeat Domains of Human ANKRA2 Deposited 2011-12-12	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 343–359（17 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	CL CHLORIDE ION × 1 NA SODIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；0.1M Bis-Tris, pH 6.5, 0.2M NaCl, 25% PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 1.57 Å R-free 0.204
4CBT Design, synthesis, and biological evaluation of potent and selective Class IIa HDAC inhibitors as a potential therapy for Huntington's disease Deposited 2013-10-16	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 648–1033（386 aa） Fragment：CATALYTIC DOMAIN, RESIDUES 648-1033	Not recorded	9F4 (1R,2R,3R)-2-[4-(5-fluoranylpyrimidin-2-yl)phenyl]-N-oxidanyl-3-phenyl-cyclopropane-1-carboxamide × 1 ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；0.1 M BISTRIS PH 6.5, 22% PEG MME 5000	Resolution 3.03 Å R-free 0.273
4CBT Design, synthesis, and biological evaluation of potent and selective Class IIa HDAC inhibitors as a potential therapy for Huntington's disease Deposited 2013-10-16	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 648–1033（386 aa） Fragment：CATALYTIC DOMAIN, RESIDUES 648-1033	Not recorded	9F4 (1R,2R,3R)-2-[4-(5-fluoranylpyrimidin-2-yl)phenyl]-N-oxidanyl-3-phenyl-cyclopropane-1-carboxamide × 1 ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；0.1 M BISTRIS PH 6.5, 22% PEG MME 5000	Resolution 3.03 Å R-free 0.273
4CBT Design, synthesis, and biological evaluation of potent and selective Class IIa HDAC inhibitors as a potential therapy for Huntington's disease Deposited 2013-10-16	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 648–1033（386 aa） Fragment：CATALYTIC DOMAIN, RESIDUES 648-1033	Not recorded	9F4 (1R,2R,3R)-2-[4-(5-fluoranylpyrimidin-2-yl)phenyl]-N-oxidanyl-3-phenyl-cyclopropane-1-carboxamide × 1 ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；0.1 M BISTRIS PH 6.5, 22% PEG MME 5000	Resolution 3.03 Å R-free 0.273
4CBY Design, synthesis, and biological evaluation of potent and selective Class IIa HDAC inhibitors as a potential therapy for Huntington's disease Deposited 2013-10-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 648–1033（386 aa） Fragment：CATALYTIC DOMAIN, RESIDUES 648-1033	Mutation：YES	KEE (1R,2R,3R)-2-[4-(1,3-oxazol-5-yl)phenyl]-N-oxidanyl-3-phenyl-cyclopropane-1-carboxamide × 1 ZN ZINC ION × 2 NA SODIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；18-24% (W/V) PEG 3350, 0.2 M NACL AND 100 MM BIS-TRIS PH 5.5	Resolution 2.72 Å R-free 0.246
4CBY Design, synthesis, and biological evaluation of potent and selective Class IIa HDAC inhibitors as a potential therapy for Huntington's disease Deposited 2013-10-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 648–1033（386 aa） Fragment：CATALYTIC DOMAIN, RESIDUES 648-1033	Mutation：YES	KEE (1R,2R,3R)-2-[4-(1,3-oxazol-5-yl)phenyl]-N-oxidanyl-3-phenyl-cyclopropane-1-carboxamide × 1 ZN ZINC ION × 2 NA SODIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；18-24% (W/V) PEG 3350, 0.2 M NACL AND 100 MM BIS-TRIS PH 5.5	Resolution 2.72 Å R-free 0.246
4CBY Design, synthesis, and biological evaluation of potent and selective Class IIa HDAC inhibitors as a potential therapy for Huntington's disease Deposited 2013-10-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 648–1033（386 aa） Fragment：CATALYTIC DOMAIN, RESIDUES 648-1033	Mutation：YES	KEE (1R,2R,3R)-2-[4-(1,3-oxazol-5-yl)phenyl]-N-oxidanyl-3-phenyl-cyclopropane-1-carboxamide × 1 ZN ZINC ION × 2 NA SODIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；18-24% (W/V) PEG 3350, 0.2 M NACL AND 100 MM BIS-TRIS PH 5.5	Resolution 2.72 Å R-free 0.246
4CBY Design, synthesis, and biological evaluation of potent and selective Class IIa HDAC inhibitors as a potential therapy for Huntington's disease Deposited 2013-10-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 648–1033（386 aa） Fragment：CATALYTIC DOMAIN, RESIDUES 648-1033	Mutation：YES	KEE (1R,2R,3R)-2-[4-(1,3-oxazol-5-yl)phenyl]-N-oxidanyl-3-phenyl-cyclopropane-1-carboxamide × 1 ZN ZINC ION × 2 NA SODIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；18-24% (W/V) PEG 3350, 0.2 M NACL AND 100 MM BIS-TRIS PH 5.5	Resolution 2.72 Å R-free 0.246
5A2S Potent, selective and CNS-penetrant tetrasubstituted cyclopropane class IIa histone deacetylase (HDAC) inhibitors Deposited 2015-05-22	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 648–1033（386 aa） Fragment：HISTONE DEACETYLASE DOMAIN, RESIDUES 648-1033	Mutation：YES	OTF (1S,2S,3S)-1-fluoranyl-2-[4-(5-fluoranylpyrimidin-2-yl)phenyl]-N-oxidanyl-3-phenyl-cyclopropane-1-carboxamide × 1 ZN ZINC ION × 2 NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions 24% W/V PEG 3350, 0.2 M AMMONIUM ACETATE, 0.1 M BIS-TRIS PH 5.5, 10 MM PROLINE	Resolution 2.65 Å R-free 0.256
5A2S Potent, selective and CNS-penetrant tetrasubstituted cyclopropane class IIa histone deacetylase (HDAC) inhibitors Deposited 2015-05-22	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 648–1033（386 aa） Fragment：HISTONE DEACETYLASE DOMAIN, RESIDUES 648-1033	Mutation：YES	OTF (1S,2S,3S)-1-fluoranyl-2-[4-(5-fluoranylpyrimidin-2-yl)phenyl]-N-oxidanyl-3-phenyl-cyclopropane-1-carboxamide × 1 ZN ZINC ION × 2 NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions 24% W/V PEG 3350, 0.2 M AMMONIUM ACETATE, 0.1 M BIS-TRIS PH 5.5, 10 MM PROLINE	Resolution 2.65 Å R-free 0.256
5ZOP Crystal structure of histone deacetylase 4 (HDAC4) in complex with a SMRT corepressor SP2 fragment Deposited 2018-04-13	Different construct Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain G 652–1050（399 aa） Fragment：UNP residues 652-1050	Mutation：H976Y	K POTASSIUM ION × 2 ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 7.5；295 K；PEG 3350, iso-propanol	Resolution 2.70 Å R-free 0.235
6FYZ Development and characterization of a CNS-penetrant benzhydryl hydroxamic acid class IIa histone deacetylase inhibitor Deposited 2018-03-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 648–1033（386 aa）	Not recorded	EBE (2~{S})-2-(2-fluorophenyl)-2-[4-(2-methylpyrimidin-5-yl)phenyl]-~{N}-oxidanyl-ethanamide × 1 ZN ZINC ION × 2 NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；0.1 M BisTris, 18 to 24% PEG MME 5000	Resolution 2.15 Å R-free 0.228
6FYZ Development and characterization of a CNS-penetrant benzhydryl hydroxamic acid class IIa histone deacetylase inhibitor Deposited 2018-03-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 648–1033（386 aa）	Not recorded	EBE (2~{S})-2-(2-fluorophenyl)-2-[4-(2-methylpyrimidin-5-yl)phenyl]-~{N}-oxidanyl-ethanamide × 1 ZN ZINC ION × 2 NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；0.1 M BisTris, 18 to 24% PEG MME 5000	Resolution 2.15 Å R-free 0.228
6FYZ Development and characterization of a CNS-penetrant benzhydryl hydroxamic acid class IIa histone deacetylase inhibitor Deposited 2018-03-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 648–1033（386 aa）	Not recorded	EBE (2~{S})-2-(2-fluorophenyl)-2-[4-(2-methylpyrimidin-5-yl)phenyl]-~{N}-oxidanyl-ethanamide × 1 ZN ZINC ION × 2 NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；0.1 M BisTris, 18 to 24% PEG MME 5000	Resolution 2.15 Å R-free 0.228
7XUZ Crystal structure of a HDAC4-MEF2A-DNA ternary complex Deposited 2022-05-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 6 PDB declaration: decameric	Chain A 62–192（131 aa） Chain B 62–192（131 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0 mM HEPES pH 7.5, 0.2 M NaCl, 3% (v/v) PEG 4000	Resolution 3.59 Å R-free 0.298

17 other PDB entries and 31 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	HDAC4_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain G； PDBConstruct 2–403； UniProt 652–1053

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	5zoo
Deposition date deposition_date	2018-04-13
Structure title title	Crystal structure of histone deacetylase 4 (HDAC4) in complex with a SMRT corepressor SP1 fragment
Keywords keywords	protein-peptide complex, HYDROLASE; HYDROLASE
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	21.15 Å
Radius of gyration Rg (electron density) rg_electron	19.92 Å
Forward intensity I(0) i0	33045200.00
Molecular weight molecular_weight	43379.0 kDa
Excluded volume excluded_volume	53832 Å³
Envelope volume envelope_volume	61140 Å³
Hydration-shell volume shell_volume	24615 Å³
Envelope diameter envelope_diameter	74.1 Å
Shell Rg shell_rg	27.54 Å
Envelope Rg envelope_rg	20.43 Å
Shape Rg shape_rg	19.90 Å
Total Rg total_rg	20.90 Å
Total atoms total_atoms	3035
Residues n_residues	401
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	72.9 Å
Rg (real space) rg_real	21.03 Å
Rg uncertainty (real space) rg_real_error	0.40 Å
I(0) (real space) i0_real	3.3050e+07
I(0) uncertainty (real space) i0_real_error	4.2110e+05
Rg (reciprocal space) rg_reciprocal	21.05 Å
I(0) (reciprocal space) i0_reciprocal	33050000.0000
Solution quality estimate total_estimate	0.8576
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	26.8 Å
Skewness Skewness skewness	0.212
Kurtosis Kurtosis kurtosis	-0.270
Angular range angular_range	— – 0.3750 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	8884000.0000
Real-space data points n_real_points	69
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.719; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.988

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	Histone deacetylase 4
Molecular weight formula_weight	43399.2 kDa
EC 编号 ec_number	3.5.1.98
Mutation mutation	H976Y
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	G
Atom count atom_count	3317

AFTTGLVYDTLMLKHQCTCGSSSSHPEHAGRIQSIWSRLQETGLRGKCECIRGRKATLEELQTVHSEAHTLLYGTNPLNRQKLDSKKLLGSLASVFVRLPCGGVGVDSDTIWNEVHSAGAARLAVGCVVELVFKVATGELKNGFAVVRPPGHHAEESTPMGFCYFNSVAVAAKLLQQRLSVSKILIVDWDVHHGNGTQQAFYSDPSVLYMSLHRYDDGNFFPGSGAPDEVGTGPGVGFNVNMAFTGGLDPPMGDAEYLAAFRTVVMPIASEFAPDVVLVSSGFDAVEGHPTPLGGYNLSARCFGYLTKQLMGLAGGRIVLALEGGYDLTAICDASEACVSALLGNELDPLPEKVLQQRPNANAVRSMEKVMEIHSKYWRCLQRTTSTAGRSLIEAQTCENEEA

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	Human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 polymer

Description description	SMRT corepressor SP1 fragment
Molecular weight formula_weight	1587.8 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A

HIRGSITQGIPRSY

来源 Source

来源生物 organism	Homo sapiens
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 3 Entity 3 non-polymer

Description description	POTASSIUM ION
Molecular weight formula_weight	39.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	279

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7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id	5zooG00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	800 — Arginase; Chain A
Homologous superfamily homologous superfamily	20 — Histone deacetylase domain

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8. Citations (1)

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Unit-cell length a length_a	131.424 Å
Unit-cell length b length_b	131.424 Å
Unit-cell length c length_c	67.770 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	6

Space group space_group	P 31 2 1
Space-group number int_tables_number	152
Crystal system crystal_system	—

Resolution resolution	1.850 Å
Low-resolution limit resolution_low	9.989 Å
R factor r_factor	0.1562
R_work r_work	0.1554
R_free r_free	0.1753

fit	/app/data/saxs_computation/zo/5zoo/5zoo.fit
pddf	/app/data/pr_computation/zo/5zoo/5zoo.pr.out
profile	/app/data/saxs_computation/zo/5zoo/5zoo.dat

Crystal structure of histone deacetylase 4 (HDAC4) in complex with a SMRT corepressor SP1 fragment

1. Protein Identity and Related Structures Protein Identity & Related Structures

Histone deacetylase 4

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)