SAXSdb — 2lq9

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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	Mutation：K60A	No other associated polymer	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

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 2LQ9	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 method 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 method 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 method 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 mutation/modification Different ligand/ion Different experimental conditions	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 mutation/modification Different experimental conditions	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 mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions	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
3CJK Crystal structure of the adduct HAH1-Cd(II)-MNK1. Deposited 2008-03-13	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 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 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）	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 mutation/modification Different oligomeric state Different ligand/ion Different experimental method 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 method 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 method 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 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 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 method 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 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）	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 mutation/modification Different ligand/ion Different experimental method 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 mutation/modification Different ligand/ion Different experimental method 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 mutation/modification Different ligand/ion Different experimental method 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 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 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
7DC1 Crystal structure of human copper homeostatic proteins atox1 Deposited 2020-10-23	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）	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
7DC1 Crystal structure of human copper homeostatic proteins atox1 Deposited 2020-10-23	Different mutation/modification Different ligand/ion Different experimental method 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；0.2M LiCl, 0.1M Tris pH8, 20% PEG6,000	Resolution 1.75 Å R-free 0.204
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 method 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 21 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

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	2lq9
Deposition date deposition_date	2012-02-28
Structure title title	Solution structure of the K60A mutant of Atox1
Keywords keywords	K60A Atox1, 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	11.21 Å
Radius of gyration Rg (electron density) rg_electron	11.05 Å
Forward intensity I(0) i0	304845000.00
Molecular weight molecular_weight	146870.0 kDa
Excluded volume excluded_volume	183850 Å³
Envelope volume envelope_volume	14990 Å³
Hydration-shell volume shell_volume	10440 Å³
Envelope diameter envelope_diameter	39.7 Å
Shell Rg shell_rg	18.06 Å
Envelope Rg envelope_rg	12.48 Å
Shape Rg shape_rg	10.98 Å
Total Rg total_rg	11.47 Å
Total atoms total_atoms	20660
Residues n_residues	1360
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	36.8 Å
Rg (real space) rg_real	11.13 Å
Rg uncertainty (real space) rg_real_error	0.23 Å
I(0) (real space) i0_real	3.0480e+08
I(0) uncertainty (real space) i0_real_error	2.8530e+06
Rg (reciprocal space) rg_reciprocal	11.13 Å
I(0) (reciprocal space) i0_reciprocal	304800000.0000
Solution quality estimate total_estimate	0.8651
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	35.9 Å
Skewness Skewness skewness	0.032
Kurtosis Kurtosis kurtosis	-0.307
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	94890.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.753; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.994; Smooth: 0.988

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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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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d2lq9a_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.17 — HMA, heavy metal-associated domain
Family Family family	d.58.17.1 — HMA, heavy metal-associated domain

CATH v4.4 (1 domains)

Domain ID domain_id	2lq9A00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	100 —

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8. Citations (1)

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Description description	Copper transport protein ATOX1
Molecular weight formula_weight	7354.5 kDa
Mutation mutation	K60A
Source method src_method	man
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	20660

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/lq/2lq9/2lq9.fit
pddf	/app/data/pr_computation/lq/2lq9/2lq9.pr.out
profile	/app/data/saxs_computation/lq/2lq9/2lq9.dat

Solution structure of the K60A mutant of 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

6. Entities and Polymers Entities & Polymers (1)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)