1yju

Solution structure of the apo form of the sixth soluble domain of Menkes protein

Method: SOLUTION NMR Dmax: 41.6 Å Quality: GOOD

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

Copper-transporting ATPase 1

Homo sapiens

UniProt Q04656

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 562–633 Fragment:Sixth soluble domain No other associated polymer 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

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.

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 2–73; UniProt 562–633

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.

SAXS scattering curve SAXS Profile

SAXS profile for 1yju

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1yju
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1yju
Deposition date deposition_date2005-01-15
Structure title titleSolution structure of the apo form of the sixth soluble domain of Menkes protein
Keywords keywords;metallochaperone, protein-protein interaction, copper(I), metal homeostasis, Structural Proteomics in Europe, SPINE, Structural Genomics, hydrolase ;; HYDROLASE
Experimental Method methodSOLUTION NMR

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

Radius of gyration Rg (Guinier) rg_guinier11.70
Radius of gyration Rg (electron density) rg_electron11.40
Forward intensity I(0) i0805085000.00
Molecular weight molecular_weight245360.0 kDa
Excluded volume excluded_volume309490 ų
Envelope volume envelope_volume19771 ų
Hydration-shell volume shell_volume12153 ų
Envelope diameter envelope_diameter46.0
Shell Rg shell_rg19.64
Envelope Rg envelope_rg14.29
Shape Rg shape_rg11.34
Total Rg total_rg11.76
Total atoms total_atoms34920
Residues n_residues2250
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3

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

Maximum dimension Dmax dmax41.6
Rg (real space) rg_real11.64
Rg uncertainty (real space) rg_real_error0.37
I(0) (real space) i0_real8.0510e+08
I(0) uncertainty (real space) i0_real_error1.0100e+07
Rg (reciprocal space) rg_reciprocal11.64
I(0) (reciprocal space) i0_reciprocal805100000.0000
Solution quality estimate total_estimate0.8083
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary15.3
Skewness Skewness skewness0.139
Kurtosis Kurtosis kurtosis-0.097
Angular range angular_range— – 0.5000 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha132500.0000
Real-space data points n_real_points80
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.502; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.997

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (1)

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (3 domains)

Domain ID domain_idd1yjua1
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.58 — Ferredoxin-like
Superfamily Superfamily superfamilyd.58.17 — HMA, heavy metal-associated domain
Family Family familyd.58.17.0 — automated matches
Domain ID domain_idd1yjua2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd1yjua3
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags

CATH v4.4 (1 domains)

Domain ID domain_id1yjuA00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily100

8. Citations (1)

9. Files and Curves (10)