SAXSdb — 5y6o

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

Death domain-associated protein 6,Transcriptional regulator ATRX

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	Insufficient information Homooligomer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain A； UniProt 1265–1288 Chain B； UniProt 1265–1288 Chain C； UniProt 1265–1288	Fragment：UNP residues 50-144,UNP residues 1265-1288	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 6.8；293 K；The DAXX 4HB_ATRX DBM fusion protein at 26 mg/ml was crystallized under conditions of 0.1M Sodium Cacodylate, pH 6.8, 1.2 M Ammonium Sulfate and 3% 1, 5- Diaminopentane Dihydrochloride, using sitting-drop vapor-diffusion method at 293K. In this process, o.5 uL of protein was mixed with 0.5 uL of mother liquor. All the crystals were soaked in a cryoprotectant made from mother liquor supplemented with 25% glycerol before flash freezing in liquid nitrogen.	Resolution 3.10 Å R-free 0.297
2	Insufficient information Homooligomer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain D； UniProt 1265–1288 Chain E； UniProt 1265–1288 Chain F； UniProt 1265–1288	Fragment：UNP residues 50-144,UNP residues 1265-1288	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 6.8；293 K；The DAXX 4HB_ATRX DBM fusion protein at 26 mg/ml was crystallized under conditions of 0.1M Sodium Cacodylate, pH 6.8, 1.2 M Ammonium Sulfate and 3% 1, 5- Diaminopentane Dihydrochloride, using sitting-drop vapor-diffusion method at 293K. In this process, o.5 uL of protein was mixed with 0.5 uL of mother liquor. All the crystals were soaked in a cryoprotectant made from mother liquor supplemented with 25% glycerol before flash freezing in liquid nitrogen.	Resolution 3.10 Å R-free 0.297
3	Insufficient information Homooligomer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain G； UniProt 1265–1288 Chain H； UniProt 1265–1288 Chain I； UniProt 1265–1288	Fragment：UNP residues 50-144,UNP residues 1265-1288	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 6.8；293 K；The DAXX 4HB_ATRX DBM fusion protein at 26 mg/ml was crystallized under conditions of 0.1M Sodium Cacodylate, pH 6.8, 1.2 M Ammonium Sulfate and 3% 1, 5- Diaminopentane Dihydrochloride, using sitting-drop vapor-diffusion method at 293K. In this process, o.5 uL of protein was mixed with 0.5 uL of mother liquor. All the crystals were soaked in a cryoprotectant made from mother liquor supplemented with 25% glycerol before flash freezing in liquid nitrogen.	Resolution 3.10 Å R-free 0.297

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 5Y6O	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2JM1 Structures and chemical shift assignments for the ADD domain of the ATRX protein Deposited 2006-09-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 159–296（138 aa） Fragment：ADD domain, residues 159-296	Not recorded	ZN ZINC ION × 3	SOLUTION NMR NMR measurement conditions pH 6.7；300 K；Ionic strength (raw mmCIF value) 0.5；Pressure ambient NMR sample composition 0.7 mM [U-15N] ADD domain 156-296, 20 mM TRIS, 1 mM DTT, 100 uM zinc chloride, 0.5 M sodium chloride, 93% H2O, 7% D2O \| 93% H2O/7% D2O NMR sample composition 0.35 mM [U-13C; U-15N] ADD domain 156-296, 20 mM TRIS, 1 mM DTT, 100 uM zinc chloride, 0.5 M sodium chloride, 93% H2O, 7% D2O \| 93% H2O/7% D2O	Resolution not provided
2LBM Solution structure of the ADD domain of ATRX complexed with histone tail H3 1-15 K9me3 Deposited 2011-04-08	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 159–296（138 aa） Fragment：UNP residues 159-296	Not recorded	ZN ZINC ION × 3	SOLUTION NMR NMR measurement conditions pH 7；300 K；Ionic strength (raw mmCIF value) 250；Pressure ambient NMR sample composition 200 uM [U-98% 13C; U-98% 15N] ATRX ADD domain-1, 200 uM H3 tail 1-15 K9me3-2, 50 mM [U-99% 2H] TRIS-3, 200 mM sodium chloride-4, 150 uM zinc sulfate-5, 1 mM [U-99% 2H] DTT-6, 95% H2O/5% D2O \| 95% H2O/5% D2O NMR sample composition 200 uM [U-98% 13C; U-98% 15N] ATRX ADD domain-7, 200 uM H3 tail 1-15 K9me3-8, 50 mM [U-99% 2H] TRIS-9, 200 mM sodium chloride-10, 150 uM zinc sulfate-11, 1 mM [U-99% 2H] DTT-12, 100% D2O \| 100% D2O	Resolution not provided
2LD1 Structures and chemical shift assignments for the ADD domain of the ATRX protein Deposited 2011-05-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 159–296（138 aa） Fragment：ADD DOMAIN, RESIDUES 159-296	Not recorded	ZN ZINC ION × 3	SOLUTION NMR NMR measurement conditions pH 6.7；300 K；Ionic strength (raw mmCIF value) 0.5；Pressure ambient NMR sample composition 0.6-0.8 mM [U-15N] ADD_domain_163-296, 20 mM [U-2H] TRIS, 1 mM [U-2H] DTT, 100 uM zinc chloride, 0.5 M sodium chloride, 95% H2O/5% D2O \| 95% H2O/5% D2O NMR sample composition 0.3-0.4 mM [U-13C; U-15N] ADD_domain_163-296, 20 mM [U-2H] TRIS, 1 mM [U-2H] DTT, 100 uM zinc chloride, 0.5 M sodium chloride, 95% H2O/5% D2O \| 95% H2O/5% D2O	Resolution not provided
3QL9 Monoclinic complex structure of ATRX ADD bound to histone H3K9me3 peptide Deposited 2011-02-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 167–289（123 aa） Fragment：N-terminal ADD domain, UNP residues 167-289	Mutation：K251R, F284Y	ZN ZINC ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.1；277 K；14% PEG 4000, 0.1M MES, 0.2 M KCL, pH 6.1, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 0.93 Å R-free 0.131
3QLA Hexagonal complex structure of ATRX ADD bound to H3K9me3 peptide Deposited 2011-02-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 167–289（123 aa） Fragment：N-terminal ADD domain, UNP residues 167-289	Mutation：K251R, F284Y	ZN ZINC ION × 3 K POTASSIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.1；277 K；14% PEG 4000, 0.1M MES, 0.2M KCL, pH 6.1, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 1.60 Å R-free 0.179
3QLA Hexagonal complex structure of ATRX ADD bound to H3K9me3 peptide Deposited 2011-02-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 167–289（123 aa） Fragment：N-terminal ADD domain, UNP residues 167-289	Mutation：K251R, F284Y	ZN ZINC ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.1；277 K；14% PEG 4000, 0.1M MES, 0.2M KCL, pH 6.1, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 1.60 Å R-free 0.179
3QLC Complex structure of ATRX ADD domain bound to unmodified H3 1-15 peptide Deposited 2011-02-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 167–289（123 aa） Fragment：N-terminal ADD domain, UNP residues 167-289	Mutation：K251R, F284Y	ZN ZINC ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；24% PEG 3350, 0.1M HEPES-NaOH, 0.2M KCL, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 2.50 Å R-free 0.241
3QLC Complex structure of ATRX ADD domain bound to unmodified H3 1-15 peptide Deposited 2011-02-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 167–289（123 aa） Fragment：N-terminal ADD domain, UNP residues 167-289	Mutation：K251R, F284Y	ZN ZINC ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；24% PEG 3350, 0.1M HEPES-NaOH, 0.2M KCL, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 2.50 Å R-free 0.241
3QLN Crystal structure of ATRX ADD domain in free state Deposited 2011-02-03	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 167–289（123 aa） Fragment：N-terminal ADD domain, UNP residues 167-289	Mutation：K251R, F284Y	ZN ZINC ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；25% (v/v) PEG 4000, 100mM HEPES-NaOH, 0.2M KCL, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 1.90 Å R-free 0.158
3QLN Crystal structure of ATRX ADD domain in free state Deposited 2011-02-03	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 167–289（123 aa） Fragment：N-terminal ADD domain, UNP residues 167-289	Mutation：K251R, F284Y	ZN ZINC ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；25% (v/v) PEG 4000, 100mM HEPES-NaOH, 0.2M KCL, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 1.90 Å R-free 0.158
4W5A Complex structure of ATRX ADD bound to H3K9me3S10ph peptide Deposited 2014-08-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 167–289（123 aa） Fragment：UNP residues 167-289	Mutation：K251R, F284Y	ZN ZINC ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；13-20% PEG 4000, 0.1 M MES, 3 mM MgCl2	Resolution 2.60 Å R-free 0.260
4W5A Complex structure of ATRX ADD bound to H3K9me3S10ph peptide Deposited 2014-08-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 167–289（123 aa） Fragment：UNP residues 167-289	Mutation：K251R, F284Y	ZN ZINC ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；13-20% PEG 4000, 0.1 M MES, 3 mM MgCl2	Resolution 2.60 Å R-free 0.260
4W5A Complex structure of ATRX ADD bound to H3K9me3S10ph peptide Deposited 2014-08-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain E 167–289（123 aa） Fragment：UNP residues 167-289	Mutation：K251R, F284Y	ZN ZINC ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；13-20% PEG 4000, 0.1 M MES, 3 mM MgCl2	Resolution 2.60 Å R-free 0.260
5GRQ Crystal Structure of DHB domain of Daxx in complex with an ATRX peptide Deposited 2016-08-12	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 1256–1285（30 aa） Fragment：DID domain, UNP residues 1256-1285 Chain D 1256–1285（30 aa） Fragment：DID domain, UNP residues 1256-1285	Not recorded	ACT ACETATE ION × 5 GOL GLYCEROL × 1 CL CHLORIDE ION × 4 ZN ZINC ION × 11	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；291 K；100mM MES 6.0, 100mM zinc acetate, 13% ethanol	Resolution 1.58 Å R-free 0.179
5Y18 Crystal structure of DAXX helical bundle domain in complex with ATRX Deposited 2017-07-19	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1268–1289（22 aa） Fragment：UNP residues 1268-1289	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；289 K；0.1M sodium citrate, pH6.5, 0.2M ammonium acetate, 30% PEG4000	Resolution 2.20 Å R-free 0.219
6G0O Crystal Structure of the first bromodomain of human BRD4 in complex with an acetylated ATRX peptide (K1030ac/K1033ac) Deposited 2018-03-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1027–1037（11 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	EDO 1,2-ETHANEDIOL × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；277 K；20.0 % PEG 6K 10.0 % EtGly 0.1 M HEPES pH 7.0 0.2 M LiCl	Resolution 1.40 Å R-free 0.166

11 other PDB entries and 16 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	ATRX_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 96–119； UniProt 1265–1288 Author chain B； PDBConstruct 96–119； UniProt 1265–1288 Author chain C； PDBConstruct 96–119； UniProt 1265–1288 Author chain D； PDBConstruct 96–119； UniProt 1265–1288 Author chain E； PDBConstruct 96–119； UniProt 1265–1288 Author chain F； PDBConstruct 96–119； UniProt 1265–1288 Author chain G； PDBConstruct 96–119； UniProt 1265–1288 Author chain H； PDBConstruct 96–119； UniProt 1265–1288 Author chain I； PDBConstruct 96–119； UniProt 1265–1288

Death domain-associated protein 6,Transcriptional regulator ATRX

Homo sapiens

UniProt Q9UER7

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Insufficient information Homooligomer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain A； UniProt 50–144 Chain B； UniProt 50–144 Chain C； UniProt 50–144	Fragment：UNP residues 50-144,UNP residues 1265-1288	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 6.8；293 K；The DAXX 4HB_ATRX DBM fusion protein at 26 mg/ml was crystallized under conditions of 0.1M Sodium Cacodylate, pH 6.8, 1.2 M Ammonium Sulfate and 3% 1, 5- Diaminopentane Dihydrochloride, using sitting-drop vapor-diffusion method at 293K. In this process, o.5 uL of protein was mixed with 0.5 uL of mother liquor. All the crystals were soaked in a cryoprotectant made from mother liquor supplemented with 25% glycerol before flash freezing in liquid nitrogen.	Resolution 3.10 Å R-free 0.297
2	Insufficient information Homooligomer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain D； UniProt 50–144 Chain E； UniProt 50–144 Chain F； UniProt 50–144	Fragment：UNP residues 50-144,UNP residues 1265-1288	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 6.8；293 K；The DAXX 4HB_ATRX DBM fusion protein at 26 mg/ml was crystallized under conditions of 0.1M Sodium Cacodylate, pH 6.8, 1.2 M Ammonium Sulfate and 3% 1, 5- Diaminopentane Dihydrochloride, using sitting-drop vapor-diffusion method at 293K. In this process, o.5 uL of protein was mixed with 0.5 uL of mother liquor. All the crystals were soaked in a cryoprotectant made from mother liquor supplemented with 25% glycerol before flash freezing in liquid nitrogen.	Resolution 3.10 Å R-free 0.297
3	Insufficient information Homooligomer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain G； UniProt 50–144 Chain H； UniProt 50–144 Chain I； UniProt 50–144	Fragment：UNP residues 50-144,UNP residues 1265-1288	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 6.8；293 K；The DAXX 4HB_ATRX DBM fusion protein at 26 mg/ml was crystallized under conditions of 0.1M Sodium Cacodylate, pH 6.8, 1.2 M Ammonium Sulfate and 3% 1, 5- Diaminopentane Dihydrochloride, using sitting-drop vapor-diffusion method at 293K. In this process, o.5 uL of protein was mixed with 0.5 uL of mother liquor. All the crystals were soaked in a cryoprotectant made from mother liquor supplemented with 25% glycerol before flash freezing in liquid nitrogen.	Resolution 3.10 Å R-free 0.297

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 5Y6O	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2KQS Phosphorylation of SUMO-interacting motif by CK2 enhances Daxx SUMO binding activity Deposited 2009-11-17	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 721–740（20 aa） Fragment：UNP residues 721-741	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.5；290 K；Ionic strength (raw mmCIF value) 0.1；Pressure ambient NMR sample composition 0.27-0.5mM [U-100% 15N] SUMO1-1, 0-1.7mM DAXX20-2, 10mM potassium phosphate-3, 100mM potassium chloride-4, 2mM DTT-5, 0.1mM EDTA-6, 0.001% sodium azide-7, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 0.5 mM [U-100% 13C; U-100% 15N] SUMO1-8, 2mM DAXX20-9, 10mM potassium phosphate-10, 100mM potassium chloride-11, 2mM DTT-12, 0.1mM EDTA-13, 0.001% sodium azide-14, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 2 mM SUMO1-15, 0.5mM [U-100% 13C; U-100% 15N] DAXX20-16, 10mM potassium phosphate-17, 100mM potassium chloride-18, 2mM DTT-19, 0.1mM EDTA-20, 0.001% sodium azide-21, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 0.5mM [U-100% 13C; U-100% 15N] SUMO1-22, 0.5mM [U-100% 13C; U-100% 15N] DAXX20-23, 10mM potassium phosphate-24, 100mM potassium chloride-25, 2mM DTT-26, 0.1mM EDTA-27, 0.001% sodium azide-28, 0.0066 w/v Pf1 phage-29, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
4H9N Complex structure 1 of DAXX/H3.3(sub5)/H4 Deposited 2012-09-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 178–389（212 aa） Fragment：UNP residues 178-389	Not recorded	PO4 PHOSPHATE ION × 9	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；1.8 M Na/K-phosphate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.95 Å R-free 0.209
4H9O Complex structure 2 of DAXX/H3.3(sub5,G90M)/H4 Deposited 2012-09-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 178–389（212 aa） Fragment：UNP residues 178-389	Not recorded	PO4 PHOSPHATE ION × 10	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；1.8 M Na/K-phosphate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.05 Å R-free 0.225
4H9P Complex structure 3 of DAXX/H3.3(sub5,G90A)/H4 Deposited 2012-09-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 178–389（212 aa） Fragment：UNP residues 178-389	Not recorded	PO4 PHOSPHATE ION × 7	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.8；277 K；1.8 M Na/K-phosphate, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.20 Å R-free 0.242
4H9P Complex structure 3 of DAXX/H3.3(sub5,G90A)/H4 Deposited 2012-09-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain C 178–389（212 aa） Fragment：UNP residues 178-389	Not recorded	PO4 PHOSPHATE ION × 14	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.8；277 K；1.8 M Na/K-phosphate, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.20 Å R-free 0.242
4H9Q Complex structure 4 of DAXX(E225A)/H3.3(sub5)/H4 Deposited 2012-09-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 178–389（212 aa） Fragment：UNP residues 178-389	Mutation：E48C	PO4 PHOSPHATE ION × 9	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；1.8 M Na/K-phosphate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.95 Å R-free 0.221
4H9Q Complex structure 4 of DAXX(E225A)/H3.3(sub5)/H4 Deposited 2012-09-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain C 178–389（212 aa） Fragment：UNP residues 178-389	Mutation：E48C	PO4 PHOSPHATE ION × 18	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；1.8 M Na/K-phosphate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.95 Å R-free 0.221
4H9R Complex structure 5 of DAXX(E225A)/H3.3(sub5,G90A)/H4 Deposited 2012-09-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 178–389（212 aa） Fragment：UNP residues 178-389	Mutation：E48A	PO4 PHOSPHATE ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.8；277 K；1.6 M Na/K-phosphate, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.20 Å R-free 0.230
4H9R Complex structure 5 of DAXX(E225A)/H3.3(sub5,G90A)/H4 Deposited 2012-09-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain C 178–389（212 aa） Fragment：UNP residues 178-389	Mutation：E48A	PO4 PHOSPHATE ION × 12	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.8；277 K；1.6 M Na/K-phosphate, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.20 Å R-free 0.230
4H9S Complex structure 6 of DAXX/H3.3(sub7)/H4 Deposited 2012-09-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain F 183–398（216 aa） Fragment：UNP residues 178-389	Not recorded	PO4 PHOSPHATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.2；293 K；0.1 M Na/K-phosphate, 2.5M NaCl, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.60 Å R-free 0.250
4H9S Complex structure 6 of DAXX/H3.3(sub7)/H4 Deposited 2012-09-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain E 183–398（216 aa） Fragment：UNP residues 178-389	Not recorded	PO4 PHOSPHATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.2；293 K；0.1 M Na/K-phosphate, 2.5M NaCl, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.60 Å R-free 0.250
4H9S Complex structure 6 of DAXX/H3.3(sub7)/H4 Deposited 2012-09-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain E 183–398（216 aa） Fragment：UNP residues 178-389 Chain F 183–398（216 aa） Fragment：UNP residues 178-389	Not recorded	PO4 PHOSPHATE ION × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.2；293 K；0.1 M Na/K-phosphate, 2.5M NaCl, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.60 Å R-free 0.250
4HGA Structure of the variant histone H3.3-H4 heterodimer in complex with its chaperone DAXX Deposited 2012-10-07	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 184–390（207 aa） Fragment：HISTONE BINDING DOMAIN, UNP RESIDUES 184-390	Not recorded	PC4 TETRACHLOROPLATINATE(II) × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.6；298 K；0.1M HEPES-Na, pH 7.6, 23% (v/v) PEG 3350, 0.25M Ammonium acetate, 1% Tacsimate pH 7.0, 6% ethanol, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 2.80 Å R-free 0.271
5GRQ Crystal Structure of DHB domain of Daxx in complex with an ATRX peptide Deposited 2016-08-12	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 55–144（90 aa） Fragment：DHB domain, UNP residues 55-144 Chain B 55–144（90 aa） Fragment：DHB domain, UNP residues 55-144	Not recorded	ACT ACETATE ION × 5 GOL GLYCEROL × 1 CL CHLORIDE ION × 4 ZN ZINC ION × 11	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；291 K；100mM MES 6.0, 100mM zinc acetate, 13% ethanol	Resolution 1.58 Å R-free 0.179
5KDM Crystal structure of EBV tegument protein BNRF1 in complex with histone chaperone DAXX and histones H3.3-H4 Deposited 2016-06-08	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 178–389（212 aa） Fragment：residues 178-389	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；295 K；0.1M MES pH 6.0, 0.8 M ammonium sulfate	Resolution 3.50 Å R-free 0.280
5Y18 Crystal structure of DAXX helical bundle domain in complex with ATRX Deposited 2017-07-19	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 55–144（90 aa） Fragment：UNP residues 55-144	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；289 K；0.1M sodium citrate, pH6.5, 0.2M ammonium acetate, 30% PEG4000	Resolution 2.20 Å R-free 0.219

11 other PDB entries and 16 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	DAXX_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–95； UniProt 50–144 Author chain B； PDBConstruct 1–95； UniProt 50–144 Author chain C； PDBConstruct 1–95； UniProt 50–144 Author chain D； PDBConstruct 1–95； UniProt 50–144 Author chain E； PDBConstruct 1–95； UniProt 50–144 Author chain F； PDBConstruct 1–95； UniProt 50–144 Author chain G； PDBConstruct 1–95； UniProt 50–144 Author chain H； PDBConstruct 1–95； UniProt 50–144 Author chain I； PDBConstruct 1–95； UniProt 50–144

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	5y6o
Deposition date deposition_date	2017-08-13
Structure title title	Crystal structure of DAXX N-terminal four-helix bundle domain (4HB) in complex with ATRX
Keywords keywords	Histone chaperone, Gene repressor, GENE REGULATION; GENE REGULATION
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	36.51 Å
Radius of gyration Rg (electron density) rg_electron	36.04 Å
Forward intensity I(0) i0	171107000.00
Molecular weight molecular_weight	106320.0 kDa
Excluded volume excluded_volume	133910 Å³
Envelope volume envelope_volume	193820 Å³
Hydration-shell volume shell_volume	46090 Å³
Envelope diameter envelope_diameter	126.8 Å
Shell Rg shell_rg	41.44 Å
Envelope Rg envelope_rg	35.02 Å
Shape Rg shape_rg	36.04 Å
Total Rg total_rg	36.50 Å
Total atoms total_atoms	7467
Residues n_residues	947
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	119.0 Å
Rg (real space) rg_real	36.50 Å
Rg uncertainty (real space) rg_real_error	1.07 Å
I(0) (real space) i0_real	1.7110e+08
I(0) uncertainty (real space) i0_real_error	2.7520e+06
Rg (reciprocal space) rg_reciprocal	36.51 Å
I(0) (reciprocal space) i0_reciprocal	171100000.0000
Solution quality estimate total_estimate	0.8929
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	41.5 Å
Skewness Skewness skewness	0.299
Kurtosis Kurtosis kurtosis	-0.509
Angular range angular_range	— – 0.2150 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	15970000.0000
Real-space data points n_real_points	44
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.905; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.988; Smooth: 0.900

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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8. Citations (1)

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Unit-cell length a length_a	78.666 Å
Unit-cell length b length_b	78.666 Å
Unit-cell length c length_c	503.215 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	54

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

Resolution resolution	3.100 Å
Low-resolution limit resolution_low	83.869 Å
R factor r_factor	0.2274
R_work r_work	0.2238
R_free r_free	0.2972

Description description	Death domain-associated protein 6,Transcriptional regulator ATRX
Molecular weight formula_weight	13686.8 kDa
EC 编号 ec_number	3.6.4.12
Source method src_method	man
Copy count entity_count	9

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H,I
Atom count atom_count	7467

Crystal structure of DAXX N-terminal four-helix bundle domain (4HB) in complex with ATRX

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

Death domain-associated protein 6,Transcriptional regulator ATRX

State in the Current Structure

Other States of the Same Protein in the Database

Death domain-associated protein 6,Transcriptional regulator ATRX

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 (1)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

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

fit	/app/data/saxs_computation/y6/5y6o/5y6o.fit
pddf	/app/data/pr_computation/y6/5y6o/5y6o.pr.out
profile	/app/data/saxs_computation/y6/5y6o/5y6o.dat