SAXSdb — 2ld1

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

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	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 159–296	Fragment：ADD DOMAIN, RESIDUES 159-296	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

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 2LD1	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 experimental conditions	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 oligomeric state Different experimental conditions	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
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 experimental method 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 method 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 experimental method 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 experimental method 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 experimental method 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 experimental method 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 experimental method 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 experimental method 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 experimental method 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 experimental method 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 method 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 ligand/ion Different experimental method 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
5Y6O Crystal structure of DAXX N-terminal four-helix bundle domain (4HB) in complex with ATRX Deposited 2017-08-13	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 Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 1265–1288（24 aa） Fragment：UNP residues 50-144,UNP residues 1265-1288 Chain B 1265–1288（24 aa） Fragment：UNP residues 50-144,UNP residues 1265-1288 Chain C 1265–1288（24 aa） Fragment：UNP residues 50-144,UNP residues 1265-1288	Not recorded	No recorded non-water small molecule	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
5Y6O Crystal structure of DAXX N-terminal four-helix bundle domain (4HB) in complex with ATRX Deposited 2017-08-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Insufficient information Homooligomer；Protein × 3 PDB declaration: trimeric	Chain D 1265–1288（24 aa） Fragment：UNP residues 50-144,UNP residues 1265-1288 Chain E 1265–1288（24 aa） Fragment：UNP residues 50-144,UNP residues 1265-1288 Chain F 1265–1288（24 aa） Fragment：UNP residues 50-144,UNP residues 1265-1288	Not recorded	No recorded non-water small molecule	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
5Y6O Crystal structure of DAXX N-terminal four-helix bundle domain (4HB) in complex with ATRX Deposited 2017-08-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 3 Insufficient information Homooligomer；Protein × 3 PDB declaration: trimeric	Chain G 1265–1288（24 aa） Fragment：UNP residues 50-144,UNP residues 1265-1288 Chain H 1265–1288（24 aa） Fragment：UNP residues 50-144,UNP residues 1265-1288 Chain I 1265–1288（24 aa） Fragment：UNP residues 50-144,UNP residues 1265-1288	Not recorded	No recorded non-water small molecule	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
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 method 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 18 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 6–142； UniProt 159–296

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	2ld1
Deposition date deposition_date	2011-05-13
Structure title title	Structures and chemical shift assignments for the ADD domain of the ATRX protein
Keywords keywords	HYDROLASE, METAL BINDING PROTEIN; METAL BINDING PROTEIN
Experimental Method method	SOLUTION NMR

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

Radius of gyration Rg (Guinier) rg_guinier	17.83 Å
Radius of gyration Rg (electron density) rg_electron	17.66 Å
Forward intensity I(0) i0	5132790000.00
Molecular weight molecular_weight	559220.0 kDa
Excluded volume excluded_volume	677600 Å³
Envelope volume envelope_volume	75728 Å³
Hydration-shell volume shell_volume	25428 Å³
Envelope diameter envelope_diameter	84.2 Å
Shell Rg shell_rg	32.18 Å
Envelope Rg envelope_rg	26.73 Å
Shape Rg shape_rg	17.69 Å
Total Rg total_rg	17.76 Å
Total atoms total_atoms	74800
Residues n_residues	4828
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	48.6 Å
Rg (real space) rg_real	16.77 Å
Rg uncertainty (real space) rg_real_error	0.10 Å
I(0) (real space) i0_real	4.8890e+09
I(0) uncertainty (real space) i0_real_error	4.5170e+07
Rg (reciprocal space) rg_reciprocal	18.03 Å
I(0) (reciprocal space) i0_reciprocal	5133000000.0000
Solution quality estimate total_estimate	0.6781
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	18.4 Å
Skewness Skewness skewness	0.405
Kurtosis Kurtosis kurtosis	-0.336
Angular range angular_range	— – 0.4450 Å⁻¹
Current regularization parameter α current_alpha	3.8570
Highest regularization parameter α highest_alpha	660600.0000
Real-space data points n_real_points	75
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.003; Oscil: 0.955; Stabil: 0.984; Sysdev: 0.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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8. Citations (1)

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Description description	Transcriptional regulator ATRX
Molecular weight formula_weight	16274.6 kDa
EC 编号 ec_number	3.6.4.12
Source method src_method	man
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	74800

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

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	3

fit	/app/data/saxs_computation/ld/2ld1/2ld1.fit
pddf	/app/data/pr_computation/ld/2ld1/2ld1.pr.out
profile	/app/data/saxs_computation/ld/2ld1/2ld1.dat

Structures and chemical shift assignments for the ADD domain of the ATRX protein

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

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

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 non-polymer

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)