SAXSdb — 7dc1

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

Copper transport protein ATOX1

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 1–68	Not recorded	AG SILVER ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；293 K；0.2M LiCl, 0.1M Tris pH8, 20% PEG6,000	Resolution 1.75 Å R-free 0.204
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 1–68	Not recorded	AG SILVER ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；293 K；0.2M LiCl, 0.1M Tris pH8, 20% PEG6,000	Resolution 1.75 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 7DC1	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1FE0 CRYSTAL STRUCTURE OF CADMIUM-HAH1 Deposited 2000-07-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–68（68 aa） Chain B 1–68（68 aa）	Not recorded	SO4 SULFATE ION × 2 CD CADMIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；MES buffer, lithium sulfate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.75 Å R-free 0.213
1FE4 CRYSTAL STRUCTURE OF MERCURY-HAH1 Deposited 2000-07-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–68（68 aa） Chain B 1–68（68 aa）	Not recorded	IUM URANYL (VI) ION × 1 SO4 SULFATE ION × 2 HG MERCURY (II) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；MES buffer, ammonium sulfate, magnesium chloride, dithiothreitol, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.75 Å R-free 0.218
1FEE CRYSTAL STRUCTURE OF COPPER-HAH1 Deposited 2000-07-21	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–68（68 aa） Chain B 1–68（68 aa）	Not recorded	CU1 COPPER (I) ION × 1 SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；Strictly anaerobic. MES buffer, lithium sulfate, and dithiothreitol, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.80 Å R-free 0.216
1TL4 Solution structure of Cu(I) HAH1 Deposited 2004-06-09	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 1–68（68 aa）	Not recorded	CU1 COPPER (I) ION × 1	SOLUTION NMR NMR measurement conditions pH 6；298 K；Ionic strength (raw mmCIF value) 10 mM sodium acetate；Pressure ambient NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 100 mM phosphate buffer；Pressure ambient NMR sample composition 1.0 mM Cu(I)HAH1 U-15N; 10 mM sodium acetate \| 90% H2O/10% D2O NMR sample composition 2 mM Cu(I)HAH1 U-95% 13C,U-98% 15N; 4 mM DTT; 100 mM phosphate buffer \| 90% H2O/10% D2O	Resolution not provided
1TL5 Solution structure of apoHAH1 Deposited 2004-06-09	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 1–68（68 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 100 mM phosphate buffer；Pressure ambient NMR sample composition 1.0 mM apoHAH1 U-15N; 5mM DTT; 100 mM phosphate buffer \| 90% H2O/10% D2O NMR sample composition 2 mM apoHAH1 U-95% 13C,U-98% 15N; 5 mM DTT; 100 mM phosphate buffer \| 90% H2O/10% D2O NMR sample composition 2 mM unlabelled apoHAH1 ; 5 mM DTT; 100 mM phosphate buffer \| 90% H2O/10% D2O	Resolution not provided
2K1R The solution NMR structure of the complex between MNK1 and HAH1 mediated by Cu(I) Deposited 2008-03-14	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 1–68（68 aa）	Not recorded	CU COPPER (II) ION × 1	SOLUTION NMR NMR measurement conditions pH 7；298 K；Pressure ambient NMR measurement conditions pH 7；298 K；Pressure ambient NMR measurement conditions pH 7；298 K；Pressure ambient NMR measurement conditions pH 7；298 K；Pressure ambient NMR sample composition 0.6 mM MNK1, 0.6 mM [U-100% 13C; U-100% 15N] HAH1, 0.6 mM COPPER(I) ION, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 0.6 mM [U-100% 13C; U-100% 15N] MNK1, 0.6 mM HAH1, 0.6 mM COPPER(I) ION, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 0.6 mM [U-100% 13C; U-100% 15N] MNK1, 1.0 mM HAH1, 1.0 mM COPPER(I) ION, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 1.0 mM MNK1, 0.6 mM [U-100% 13C; U-100% 15N] HAH1, 1.0 mM COPPER(I) ION, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
2LQ9 Solution structure of the K60A mutant of Atox1 Deposited 2012-02-28	Different mutation/modification 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 1–68（68 aa）	Mutation：K60A	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 0.215；Pressure ambient NMR sample composition 0.4-0.5 mM [U-100% 13C; U-100% 15N] entity-1, 100 mM sodium phosphate-2, 2-2.5 mM DTT-3, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 0.4-0.5 mM [U-100% 15N] entity-4, 100 mM sodium phosphate-5, 2-2.5 mM DTT-6, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 0.4-0.5 mM [U-100% 13C; U-100% 15N] entity-7, 100 mM sodium phosphate-8, 2-2.5 mM DTT-9, 100% D2O \| 100% D2O	Resolution not provided
3CJK Crystal structure of the adduct HAH1-Cd(II)-MNK1. Deposited 2008-03-13	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2–68（67 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.7；298 K；0.1 M sodium citrate, 20% PEG-6000, pH 4.7, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 1.80 Å R-free 0.283
3IWL Crystal structure of cisplatin bound to a human copper chaperone (monomer) Deposited 2009-09-02	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–68（68 aa）	Not recorded	PT PLATINUM (II) ION × 1 SO4 SULFATE ION × 1 TCE 3,3',3''-phosphanetriyltripropanoic acid × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；294 K；2M lithium sulfate, 0.1M MES, pH 6, VAPOR DIFFUSION, HANGING DROP, temperature 294K	Resolution 1.60 Å R-free 0.210
3IWL Crystal structure of cisplatin bound to a human copper chaperone (monomer) Deposited 2009-09-02	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–68（68 aa）	Not recorded	PT PLATINUM (II) ION × 2 SO4 SULFATE ION × 2 TCE 3,3',3''-phosphanetriyltripropanoic acid × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；294 K；2M lithium sulfate, 0.1M MES, pH 6, VAPOR DIFFUSION, HANGING DROP, temperature 294K	Resolution 1.60 Å R-free 0.210
3IWX Crystal structure of cisplatin bound to a human copper chaperone (dimer) Deposited 2009-09-03	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–68（68 aa） Chain B 1–68（68 aa）	Not recorded	CPT Cisplatin × 1 SO4 SULFATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；294 K；1.5 M lithium sulfate, 0.1M MES, 50 mM NaCl, pH 6, VAPOR DIFFUSION, HANGING DROP, temperature 294K	Resolution 2.14 Å R-free 0.228
4QOT Crystal structure of human copper chaperone bound to the platinum ion Deposited 2014-06-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–68（68 aa） Chain B 1–68（68 aa）	Not recorded	PT PLATINUM (II) ION × 2 SO4 SULFATE ION × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；12mg/mlATOX-Pt(DACH)(H2O)(SO4), 65% sat Li2SO4, 100mM MES, 60mM NaCl, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.20 Å R-free 0.239
4YDX Crystal structure of cisplatin bound to a human copper chaperone (monomer) - new refinement Deposited 2015-02-23	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2–68（67 aa）	Not recorded	PT PLATINUM (II) ION × 1 SO4 SULFATE ION × 1 TCE 3,3',3''-phosphanetriyltripropanoic acid × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；294 K；2M lithium sulfate, 0.1M MES, pH 6, VAPOR DIFFUSION, HANGING DROP, temperature 294K	Resolution 1.60 Å R-free 0.155
4YEA Crystal structure of cisplatin bound to a human copper chaperone (dimer) - new refinement Deposited 2015-02-23	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 2–68（67 aa） Chain B 2–68（67 aa）	Not recorded	CU COPPER (II) ION × 1 SO4 SULFATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；294 K；1.5 M LITHIUM SULFATE, 0.1M MES, 50 MM NACL, PH 6, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 294K	Resolution 2.14 Å R-free 0.197
5F0W Crystal structure of human copper homeostatic proteins atox1 Deposited 2015-11-28	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–68（68 aa）	Not recorded	AG SILVER ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.2 M tri-sodium citrate, 20 % (W/V) PEG 3350	Resolution 2.70 Å R-free 0.289
5F0W Crystal structure of human copper homeostatic proteins atox1 Deposited 2015-11-28	Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–68（68 aa）	Not recorded	AG SILVER ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.2 M tri-sodium citrate, 20 % (W/V) PEG 3350	Resolution 2.70 Å R-free 0.289
5F0W Crystal structure of human copper homeostatic proteins atox1 Deposited 2015-11-28	Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 1–68（68 aa）	Not recorded	AG SILVER ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.2 M tri-sodium citrate, 20 % (W/V) PEG 3350	Resolution 2.70 Å R-free 0.289
5F0W Crystal structure of human copper homeostatic proteins atox1 Deposited 2015-11-28	Different experimental conditions Different structure-quality metrics	Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 1–68（68 aa）	Not recorded	AG SILVER ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.2 M tri-sodium citrate, 20 % (W/V) PEG 3350	Resolution 2.70 Å R-free 0.289
5T7L Pt(II)-mediated copper-dependent interactions between ATOX1 and MNK1 Deposited 2016-09-05	Different construct 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 2–68（67 aa）	Not recorded	PT PLATINUM (II) ION × 2 CU COPPER (II) ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；PEG-6000 10 to 30 % w/v and sodium citrate 0.1M at pH 4.7	Resolution 2.83 Å R-free 0.273
7ZC3 Crystal structure of human copper chaperone Atox1 bound to zinc ion by CxxC motif Deposited 2022-03-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–68（68 aa） Chain B 1–68（68 aa）	Not recorded	ZN ZINC ION × 1 SO4 SULFATE ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；Drop:12.5mg/ml Atox1 + 1.62mM ZnSO4 in 25mM Sodium Phosphate buffer pH 7.0, 2mM DTT; Reservoir: 1.9M Li2SO4, 100mM MES pH 6.0, 2.5% glycerol; VAPOR DIFFUSION, SITTING DROP, temperature 293K.	Resolution 1.90 Å R-free 0.186

16 other PDB entries and 20 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	ATOX1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–68； UniProt 1–68 Author chain B； PDBConstruct 1–68； UniProt 1–68

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	7dc1
Deposition date deposition_date	2020-10-23
Structure title title	Crystal structure of human copper homeostatic proteins atox1
Keywords keywords	protein binding, copper ion binding, ATPase binding, METAL TRANSPORT; METAL TRANSPORT
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	15.05 Å
Radius of gyration Rg (electron density) rg_electron	13.92 Å
Forward intensity I(0) i0	4758830.00
Molecular weight molecular_weight	14976.0 kDa
Excluded volume excluded_volume	18402 Å³
Envelope volume envelope_volume	20168 Å³
Hydration-shell volume shell_volume	12325 Å³
Envelope diameter envelope_diameter	45.4 Å
Shell Rg shell_rg	19.62 Å
Envelope Rg envelope_rg	14.07 Å
Shape Rg shape_rg	13.87 Å
Total Rg total_rg	15.13 Å
Total atoms total_atoms	1014
Residues n_residues	134
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	47.4 Å
Rg (real space) rg_real	14.93 Å
Rg uncertainty (real space) rg_real_error	0.21 Å
I(0) (real space) i0_real	4.7590e+06
I(0) uncertainty (real space) i0_real_error	5.2410e+04
Rg (reciprocal space) rg_reciprocal	14.94 Å
I(0) (reciprocal space) i0_reciprocal	4759000.0000
Solution quality estimate total_estimate	0.8103
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	19.8 Å
Skewness Skewness skewness	0.089
Kurtosis Kurtosis kurtosis	-0.394
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	663000.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.847; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.990; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Copper transport protein ATOX1
Molecular weight formula_weight	7412.6 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	1156

MPKHEFSVDMTCGGCAEAVSRVLNKLGGVKYDIDLPNKKVCIESEHSMDTLLATLKKTGKTVSYLGLE

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 non-polymer

Description description	SILVER ION
Molecular weight formula_weight	107.9 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	133

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8. Citations (1)

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Unit-cell length a length_a	104.493 Å
Unit-cell length b length_b	104.493 Å
Unit-cell length c length_c	29.188 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	12

Space group space_group	P 32 2 1
Space-group number int_tables_number	154
Crystal system crystal_system	—

Resolution resolution	1.750 Å
Low-resolution limit resolution_low	19.473 Å
R factor r_factor	—
R_work r_work	0.1810
R_free r_free	0.2041

fit	/app/data/saxs_computation/dc/7dc1/7dc1.fit
pddf	/app/data/pr_computation/dc/7dc1/7dc1.pr.out
profile	/app/data/saxs_computation/dc/7dc1/7dc1.dat

Crystal structure of human copper homeostatic proteins atox1

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

Copper transport protein ATOX1

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