SAXSdb — 7lu8

▼

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

Copper-transporting ATPase 1

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 84–156	Not recorded	No other associated polymer	SOLUTION NMR NMR measurement conditions：pH 7.4；298 K；Ionic strength (raw mmCIF value) 210；Pressure 1 NMR sample composition：0.35 mM [U-13C; U-15N] HMA2A, 50 mM HEPES, 150 mM sodium chloride, 5 mM TCEP, 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 7LU8	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1AW0 FOURTH METAL-BINDING DOMAIN OF THE MENKES COPPER-TRANSPORTING ATPASE, NMR, 20 STRUCTURES Deposited 1997-10-08	Different construct Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 375–446（72 aa） Fragment：FOURTH METAL-BINDING DOMAIN	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.8；300 K	Resolution not provided
1KVI Solution Structure of the Reduced Form of the First Heavy Metal Binding Motif of the Menkes Protein Deposited 2002-01-26	Different construct Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–79（79 aa） Fragment：RESIDUES 1-79	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.5；298 K；Pressure 1 NMR sample composition 20 mM NaAcetate buffer, 10 mM DTT, 1 mM EDTA, 0.01% Na Azide, 1 mM Protein \| H2O/D2O	Resolution not provided
1KVJ Solution Structure of the Cu(I) bound form of the first heavy metal binding motif of the Menkes protein Deposited 2002-01-26	Different construct Different ligand/ion Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–79（79 aa） Fragment：RESIDUES 1-79	Not recorded	CU1 COPPER (I) ION × 1	SOLUTION NMR NMR measurement conditions pH 6.5；295 K；Pressure 1 NMR sample composition 20 mM Na Acetate buffer, 10 mM DTT, 1 mM EDTA, 0.01% Na Azide, 1 mM Protein \| H2O/D2O	Resolution not provided
1Q8L Second Metal Binding Domain of the Menkes ATPase Deposited 2003-08-21	Different construct Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 164–246（83 aa） Fragment：Second Copper Binding Domain (residues 164-246)	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.5；298 K；Ionic strength (raw mmCIF value) 30mM；Pressure ambient NMR sample composition 0.5mM MNKr2, U-15N, 20mM potassium phosphate, 10 mM Sodium Chloride, pH6.5. \| 90% H2O/10% D2O	Resolution not provided
1S6O Solution structure and backbone dynamics of the apo-form of the second metal-binding domain of the Menkes protein ATP7A Deposited 2004-01-26	Different construct Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 169–240（72 aa） Fragment：Second soluble domain	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) phosphate 100 mM；Pressure ambient NMR sample composition 1 mM protein, pH 7 \| 90% H2O/10% D2O NMR sample composition 1 mM protein U-15N, pH 7 \| 90% H2O/10% D2O NMR sample composition 1 mM protein U-15N,13C, pH 7 \| 90% H2O/10% D2O	Resolution not provided
1S6U Solution structure and backbone dynamics of the Cu(I) form of the second metal-binding domain of the Menkes protein ATP7A Deposited 2004-01-27	Different construct Different ligand/ion Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 169–240（72 aa） Fragment：Second domain of ATP7A	Not recorded	CU1 COPPER (I) ION × 1	SOLUTION NMR NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 100 mM phosphate；Pressure ambient NMR sample composition 1 mM protein, 1:1 copper(I) \| 90% H2O/10% D2O NMR sample composition 1 mM protein U-15N, 1:1 copper(I) \| 90% H2O/10% D2O NMR sample composition 1 mM protein U-15N,13C, 1:1 copper(I) \| 90% H2O/10% D2O	Resolution not provided
1Y3J Solution structure of the copper(I) form of the fifth domain of Menkes protein Deposited 2004-11-25	Different construct Different ligand/ion Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 486–558（73 aa） Fragment：fifth domain of the menkes protein	Not recorded	CU COPPER (II) ION × 1	SOLUTION NMR NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 50mM sodium phosphate；Pressure ambient NMR sample composition 1mM MNK5 domain U-15N,13C; 50mM phosphate buffer NA \| 90% H2O/10% D2O	Resolution not provided
1Y3K Solution structure of the apo form of the fifth domain of Menkes protein Deposited 2004-11-25	Different construct Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 486–558（73 aa） Fragment：fifth domain of the menkes protein	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 50mM sodium phosphate；Pressure ambient NMR sample composition 1mM MNK5 domain U-15N,13C; 50mM phosphate buffer NA \| 90% H2O/10% D2O	Resolution not provided
1YJR Solution structure of the apo form of the sixth soluble domain A69P mutant of Menkes protein Deposited 2005-01-15	Different construct Different mutation/modification Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 562–633（72 aa） Fragment：Sixth soluble domain	Mutation：A69P	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 0.8mM 15N labeled sample; 5mM DTT; 100mM phosphate buffer \| 90% H2O/10% D2O NMR sample composition 0.8mM 15N 13C labeled sample; 5mM DTT; 100mM phosphate buffer \| 90% H2O/10% D2O NMR sample composition 1.0mM unlabeled sample; 5mM DTT; 100mM phosphate buffer \| 90% H2O/10% D2O	Resolution not provided
1YJT Solution structure of the Cu(I) form of the sixth soluble domain A69P mutant of Menkes protein Deposited 2005-01-15	Different construct Different mutation/modification Different ligand/ion Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 562–633（72 aa） Fragment：Sixth soluble domain	Mutation：A69P	CU1 COPPER (I) ION × 1	SOLUTION NMR NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 100mM phosphate buffer；Pressure ambient NMR sample composition 0.8mM 15N labeled sample; 5mM DTT; 100mM phosphate buffer \| 90% H2O/10% D2O NMR sample composition 0.8mM 15N 13C labeled sample; 5mM DTT; 100mM phosphate buffer \| 90% H2O/10% D2O NMR sample composition 1.0mM unlabeled sample; 5mM DTT; 100mM phosphate buffer \| 90% H2O/10% D2O	Resolution not provided
1YJU Solution structure of the apo form of the sixth soluble domain of Menkes protein Deposited 2005-01-15	Different construct Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 562–633（72 aa） Fragment：Sixth soluble domain	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 100mM phosphate buffer；Pressure ambient NMR sample composition 0.8mM 15N labeled sample; 5mM DTT; 100mM phosphate buffer \| 90% H2O/10% D2O NMR sample composition 0.8mM 15N 13C labeled sample; 5mM DTT; 100mM phosphate buffer \| 90% H2O/10% D2O NMR sample composition 1.0mM unlabeled sample; 5mM DTT; 100mM phosphate buffer \| 90% H2O/10% D2O	Resolution not provided
1YJV Solution structure of the Cu(I) form of the sixth soluble domain of Menkes protein Deposited 2005-01-15	Different construct Different ligand/ion Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 562–633（72 aa） Fragment：Sixth soluble domain	Not recorded	CU1 COPPER (I) ION × 1	SOLUTION NMR NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 100mM phosphate buffer；Pressure ambient NMR sample composition 0.8mM 15N labeled sample; 5mM DTT; 100mM phosphate buffer \| 90% H2O/10% D2O NMR sample composition 0.8mM 15N 13C labeled sample; 5mM DTT; 100mM phosphate buffer \| 90% H2O/10% D2O NMR sample composition 1.0mM unlabeled sample; 5mM DTT; 100mM phosphate buffer \| 90% H2O/10% D2O	Resolution not provided
2AW0 FOURTH METAL-BINDING DOMAIN OF THE MENKES COPPER-TRANSPORTING ATPASE, NMR, 20 STRUCTURES Deposited 1997-10-08	Different construct Different ligand/ion Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 375–446（72 aa） Fragment：FOURTH METAL-BINDING DOMAIN	Not recorded	AG SILVER ION × 1	SOLUTION NMR NMR measurement conditions pH 6.8；300 K	Resolution not provided
2G9O Solution structure of the apo form of the third metal-binding domain of ATP7A protein (Menkes Disease protein) Deposited 2006-03-07	Different construct Different mutation/modification Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 275–352（78 aa） Fragment：sixth soluble domain, residues 275-352	Mutation：K46V	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 100mM phosphate buffer；Pressure ambient NMR sample composition 1.5mM Apo-MNK3 unlabelled sample, 100mM phosphate buffer, pH 7.0, 1mM DTT,90% H2O, 10% D2O \| 90% H2O/10% D2O NMR sample composition 1mM Apo-MNK3 15N labelled sample, 100mM phosphate buffer, pH 7.0, 1mM DTT, 90% H2O, 10% D2O \| 90% H2O/10% D2O NMR sample composition 1mM Apo-MNK3 15N, 13C labelled sample, 100mM phosphate buffer, pH 7.0, 1mM DTT, 90% H2O, 10% D2O \| 90% H2O/10% D2O	Resolution not provided
2GA7 Solution structure of the copper(I) form of the third metal-binding domain of ATP7A protein (menkes disease protein) Deposited 2006-03-08	Different construct Different mutation/modification Different ligand/ion Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 275–352（78 aa） Fragment：Third soluble domain, residues 275-352	Mutation：K46V	CU1 COPPER (I) ION × 1	SOLUTION NMR NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 100mM phosphate buffer；Pressure ambient NMR sample composition 1mM copper(I)MNK3 unlabelled sample, 100mM phosphate buffer, pH 7.0, 90% H2O, 10% D2O \| 90% H2O/10% D2O NMR sample composition 0.5mM copper(I)MNK3 15N labeled sample, 100mM phosphate buffer, pH 7.0, 90% H2O, 10% D2O \| 90% H2O/10% D2O NMR sample composition 0.5mM copper(I)MNK3 15N,13C labeled sample, 100mM phosphate buffer, pH 7.0, 90% H2O, 10% D2O \| 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 construct Different oligomeric state Different ligand/ion Different experimental conditions	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 5–77（73 aa） Fragment：HMA 1 domain: Residues 5-77	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
2KIJ Solution structure of the Actuator domain of the copper-transporting ATPase ATP7A Deposited 2009-05-06	Different construct Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 806–924（119 aa） Fragment：actuator domain, UNP residues 806-924	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) phosphate, arginine, glutamate；Pressure ambient NMR sample composition 0.3 mM Actd-1, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 0.3 mM [U-13C; U-15N] Actd-2, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 0.3 mM [U-15N] Actd-3, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
2KMV Solution structure of the nucleotide binding domain of the human Menkes protein in the ATP-free form Deposited 2009-08-05	Different construct Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1051–1231（181 aa） Fragment：nucleotide binding domain	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) phospate 0.05；Pressure ambient NMR sample composition 1.5 mM [U-99% 15N] ATPfree N-MNK-1, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 0.8 mM [U-95% 13C; U-95% 15N] ATPfree N-MNK-2, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
2KMX Solution structure of the nucleotide binding domain of the human Menkes protein in the ATP-bound form Deposited 2009-08-05	Different construct Different ligand/ion Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1051–1231（181 aa） Fragment：nucleotide binding domain	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 1	SOLUTION NMR NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) phospate 0.05；Pressure ambient NMR sample composition 1.5 mM [U-99% 15N] ATPfree N-MNK-1, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 0.8 mM [U-95% 13C; U-95% 15N] ATPfree N-MNK-2, 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 ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 7–77（71 aa）	Not recorded	CD CADMIUM ION × 1	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
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 method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 7–77（71 aa） Fragment：UNP residues 7-77	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

21 other PDB entries and 21 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	ATP7A_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–76； UniProt 84–156

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	7lu8
Deposition date deposition_date	2021-02-21
Structure title title	Structure of the cryptic HMA domain of the human copper transporter ATP7A
Keywords keywords	copper transport, heavy metal associated domain, ATP7A, membrane transporter, METAL TRANSPORT; METAL TRANSPORT
Experimental Method method	SOLUTION NMR

▼

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

Radius of gyration Rg (Guinier) rg_guinier	13.25 Å
Radius of gyration Rg (electron density) rg_electron	13.10 Å
Forward intensity I(0) i0	338358000.00
Molecular weight molecular_weight	167180.0 kDa
Excluded volume excluded_volume	215070 Å³
Envelope volume envelope_volume	38541 Å³
Hydration-shell volume shell_volume	17671 Å³
Envelope diameter envelope_diameter	58.1 Å
Shell Rg shell_rg	24.78 Å
Envelope Rg envelope_rg	19.26 Å
Shape Rg shape_rg	13.04 Å
Total Rg total_rg	13.74 Å
Total atoms total_atoms	24380
Residues n_residues	1520
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

▼

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	49.9 Å
Rg (real space) rg_real	13.28 Å
Rg uncertainty (real space) rg_real_error	0.48 Å
I(0) (real space) i0_real	3.3840e+08
I(0) uncertainty (real space) i0_real_error	4.1170e+06
Rg (reciprocal space) rg_reciprocal	13.28 Å
I(0) (reciprocal space) i0_reciprocal	338400000.0000
Solution quality estimate total_estimate	0.6685
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	15.8 Å
Skewness Skewness skewness	0.469
Kurtosis Kurtosis kurtosis	0.361
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	187200.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.244; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.955; Smooth: 0.000

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (1)

▶

8. Citations (1)

▶

Description description	Copper-transporting ATPase 1
Molecular weight formula_weight	8367.7 kDa
EC 编号 ec_number	7.2.2.8
Source method src_method	man
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	24380

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/lu/7lu8/7lu8.fit
pddf	/app/data/pr_computation/lu/7lu8/7lu8.pr.out
profile	/app/data/saxs_computation/lu/7lu8/7lu8.dat

Structure of the cryptic HMA domain of the human copper transporter ATP7A

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

Copper-transporting ATPase 1

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

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)