1y3j

Solution structure of the copper(I) form of the fifth domain of Menkes protein

Method: SOLUTION NMR Dmax: 31.9 Å Quality: REASONABLE

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 486–558 Fragment:fifth domain of the menkes protein 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

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 1–73; UniProt 486–558

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 1y3j

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1y3j
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1y3j
Deposition date deposition_date2004-11-25
Structure title titleSolution structure of the copper(I) form of the fifth domain of Menkes protein
Keywords keywords;ferrodoxin-like fold, beta-alpha-beta-beta-alpha-beta structure, 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_guinier12.66
Radius of gyration Rg (electron density) rg_electron12.12
Forward intensity I(0) i0427719000.00
Molecular weight molecular_weight170830.0 kDa
Excluded volume excluded_volume212480 ų
Envelope volume envelope_volume25588 ų
Hydration-shell volume shell_volume13817 ų
Envelope diameter envelope_diameter53.7
Shell Rg shell_rg21.86
Envelope Rg envelope_rg16.96
Shape Rg shape_rg12.06
Total Rg total_rg12.55
Total atoms total_atoms23880
Residues n_residues1540
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 dmax31.9
Rg (real space) rg_real11.99
Rg uncertainty (real space) rg_real_error0.04
I(0) (real space) i0_real4.0870e+08
I(0) uncertainty (real space) i0_real_error3.0800e+06
Rg (reciprocal space) rg_reciprocal12.66
I(0) (reciprocal space) i0_reciprocal427700000.0000
Solution quality estimate total_estimate0.6815
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary16.2
Skewness Skewness skewness0.066
Kurtosis Kurtosis kurtosis-0.358
Angular range angular_range— – 0.5000 −1
Current regularization parameter α current_alpha2.9100
Highest regularization parameter α highest_alpha109200.0000
Real-space data points n_real_points80
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.001; Oscil: 0.978; Stabil: 0.979; Sysdev: 0.000; Positv: 1.000; Valcen: 0.990; Smooth: 0.000

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (2)

7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd1y3ja1
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_idd1y3ja2
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_id1y3jA00
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)