3v31

Crystal Structure of the Peptide Bound Complex of the Ankyrin Repeat Domains of Human ANKRA2

Method: X-RAY DIFFRACTION D_max: 69.1 Å Quality: REASONABLE

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

Ankyrin repeat family A protein 2

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 A； UniProt 148–313	Fragment：UNP residues 148-313 (ANK repeats)	Histone deacetylase 4 × 1 （P56524） 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

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 3V31	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3SO8 Crystal Structure of ANKRA Deposited 2011-06-30	Different construct 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 149–310（162 aa） Fragment：UNP residues 149-310	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；300 K；Peg 3350, pH 6, VAPOR DIFFUSION, SITTING DROP, temperature 300K	Resolution 1.90 Å R-free 0.255
3V2O Crystal Structure of the Peptide Bound Complex of the Ankyrin Repeat Domains of Human ANKRA2 Deposited 2011-12-12	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 148–313（166 aa） Fragment：UNP residues 148-313 (ANK repeats)	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；0.1M Hepes, pH 7.5, 0.2M ammonium acetate, 25% PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 1.89 Å R-free 0.269
3V2X Crystal Structure of the Peptide Bound Complex of the Ankyrin Repeat Domains of Human ANKRA2 Deposited 2011-12-12	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 148–313（166 aa） Fragment：UNP residues 148-313 (ANK repeats)	Not recorded	No recorded non-water small molecule	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 1.85 Å R-free 0.213
4LG6 Crystal structure of ANKRA2-CCDC8 complex Deposited 2013-06-27	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 142–313（172 aa）	Not recorded	UNX UNKNOWN LIGAND × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；291 K；25% PEG3350, 0.2 M sodium chloride, 0.1 M HEPES, pH 7.5, vapor diffusion, temperature 291K	Resolution 1.80 Å R-free 0.208
4QQI Crystal structure of ANKRA2-RFX7 complex Deposited 2014-06-27	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 142–313（172 aa） Fragment：UNP residues 142-313	Not recorded	SO4 SULFATE ION × 4 UNX UNKNOWN LIGAND × 11 UNL UNKNOWN LIGAND × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；291 K；0.1 M sodium hepes, 2.0 M ammonium sulfate, 2% PEG 400, pH 7.5, vapor diffusion, temperature 291K	Resolution 2.03 Å R-free 0.269
8CXG Structures of Zika Virus in Complex with Antibodies Targeting E Dimer Epitopes and Basis for Neutralization Efficacy Deposited 2022-05-21	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 12 PDB declaration: dodecameric	Chain A 1–135（135 aa） Chain B 1–135（135 aa） Chain C 1–135（135 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.20 Å
8CXH Structures of Zika Virus in Complex with Antibodies Targeting E Dimer Epitopes and Basis for Neutralization Efficacy Deposited 2022-05-21	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 10 PDB declaration: decameric	Chain A 1–135（135 aa） Chain B 1–135（135 aa） Chain C 1–135（135 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.20 Å
8CXI Structures of Zika Virus in Complex with Antibodies Targeting E Dimer Epitopes and Basis for Neutralization Efficacy Deposited 2022-05-21	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 10 PDB declaration: decameric	Chain A 1–135（135 aa） Chain B 1–135（135 aa） Chain C 1–135（135 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.40 Å

8 other PDB entries and 8 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	ANRA2_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–167； UniProt 148–313

Histone deacetylase 4

OrganismNot specified

UniProt P56524

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 B； UniProt 343–359	Non-standard monomer：Yes (specific site not provided by mmCIF)	Ankyrin repeat family A protein 2 × 1 （Q9H9E1） 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

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 3V31	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 ligand/ion 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 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 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 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 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 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
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
5ZOO Crystal structure of histone deacetylase 4 (HDAC4) in complex with a SMRT corepressor SP1 fragment Deposited 2018-04-13	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 G 652–1053（402 aa） Fragment：UNP residues 652-1052	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 1.85 Å R-free 0.175
5ZOP Crystal structure of histone deacetylase 4 (HDAC4) in complex with a SMRT corepressor SP2 fragment Deposited 2018-04-13	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 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	2
Chains and sequence ranges	Author chain B； PDBConstruct 2–18； UniProt 343–359

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	3v31
Deposition date deposition_date	2011-12-12
Structure title title	Crystal Structure of the Peptide Bound Complex of the Ankyrin Repeat Domains of Human ANKRA2
Keywords keywords	Structural Genomics Consortium, SGC, ANKRA2, ANK repeat, PROTEIN BINDING, HDAC4; PROTEIN BINDING
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	18.31 Å
Radius of gyration Rg (electron density) rg_electron	17.68 Å
Forward intensity I(0) i0	7242910.00
Molecular weight molecular_weight	19845.0 kDa
Excluded volume excluded_volume	24918 Å³
Envelope volume envelope_volume	29283 Å³
Hydration-shell volume shell_volume	14618 Å³
Envelope diameter envelope_diameter	68.8 Å
Shell Rg shell_rg	23.06 Å
Envelope Rg envelope_rg	18.40 Å
Shape Rg shape_rg	17.67 Å
Total Rg total_rg	18.62 Å
Total atoms total_atoms	1391
Residues n_residues	183
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	69.1 Å
Rg (real space) rg_real	18.40 Å
Rg uncertainty (real space) rg_real_error	0.56 Å
I(0) (real space) i0_real	7.2430e+06
I(0) uncertainty (real space) i0_real_error	9.9990e+04
Rg (reciprocal space) rg_reciprocal	18.39 Å
I(0) (reciprocal space) i0_reciprocal	7243000.0000
Solution quality estimate total_estimate	0.7201
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	19.6 Å
Skewness Skewness skewness	0.559
Kurtosis Kurtosis kurtosis	0.063
Angular range angular_range	— – 0.4350 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	3461000.0000
Real-space data points n_real_points	75
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.521; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.793; Smooth: 0.000

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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	Ankyrin repeat family A protein 2
Molecular weight formula_weight	18171.6 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	1533

GANSLSVHQLAAQGEMLYLATRIEQENVINHTDEEGFTPLMWAAAHGQIAVVEFLLQNGADPQLLGKGRESALSLACSKGYTDIVKMLLDCGVDVNEYDWNGGTPLLYAVHGNHVKCVKMLLESGADPTIETDSGYNSMDLAVALGYRSVQQVIESHLLKLLQNIKE

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

Entity 2 Entity 2 polymer

Description description	Histone deacetylase 4
Molecular weight formula_weight	1822.2 kDa
EC 编号 ec_number	3.5.1.98
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

XLPLYTSPSLPNITLGLP

Entity 3 Entity 3 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 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	139

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7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id	3v31A00
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily	20 — Ankyrin repeat-containing domain

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8. Citations (1)

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Unit-cell length a length_a	29.663 Å
Unit-cell length b length_b	52.822 Å
Unit-cell length c length_c	51.556 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	98.01 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	2

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	1.570 Å
Low-resolution limit resolution_low	26.410 Å
R factor r_factor	0.1759
R_work r_work	0.1744
R_free r_free	0.2045

fit	/app/data/saxs_computation/v3/3v31/3v31.fit
pddf	/app/data/pr_computation/v3/3v31/3v31.pr.out
profile	/app/data/saxs_computation/v3/3v31/3v31.dat

Crystal Structure of the Peptide Bound Complex of the Ankyrin Repeat Domains of Human ANKRA2

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

Ankyrin repeat family A protein 2

State in the Current Structure

Other States of the Same Protein in the Database

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

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)