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Yorodumi- PDB-1kvi: Solution Structure of the Reduced Form of the First Heavy Metal B... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1kvi | ||||||
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Title | Solution Structure of the Reduced Form of the First Heavy Metal Binding Motif of the Menkes Protein | ||||||
Components | Copper-transporting ATPase 1 | ||||||
Keywords | HYDROLASE / MENKES / Cu-Protein | ||||||
Function / homology | Function and homology information peptidyl-lysine modification / epinephrine metabolic process / elastin biosynthetic process / positive regulation of response to wounding / tryptophan metabolic process / cellular response to cobalt ion / Ion influx/efflux at host-pathogen interface / positive regulation of tyrosinase activity / copper-dependent protein binding / cerebellar Purkinje cell differentiation ...peptidyl-lysine modification / epinephrine metabolic process / elastin biosynthetic process / positive regulation of response to wounding / tryptophan metabolic process / cellular response to cobalt ion / Ion influx/efflux at host-pathogen interface / positive regulation of tyrosinase activity / copper-dependent protein binding / cerebellar Purkinje cell differentiation / elastic fiber assembly / response to iron(III) ion / copper ion transmembrane transporter activity / P-type divalent copper transporter activity / P-type monovalent copper transporter activity / P-type Cu+ transporter / positive regulation of melanin biosynthetic process / superoxide dismutase copper chaperone activity / cellular response to lead ion / pyramidal neuron development / copper ion export / copper ion import / copper ion homeostasis / copper ion transport / melanosome membrane / catecholamine metabolic process / serotonin metabolic process / detoxification of copper ion / norepinephrine metabolic process / trans-Golgi network transport vesicle / regulation of oxidative phosphorylation / T-helper cell differentiation / positive regulation of vascular associated smooth muscle cell migration / collagen fibril organization / cartilage development / response to manganese ion / negative regulation of iron ion transmembrane transport / cellular response to antibiotic / skin development / pigmentation / hair follicle morphogenesis / dopamine metabolic process / lung alveolus development / response to zinc ion / cellular response to platelet-derived growth factor stimulus / positive regulation of catalytic activity / cell leading edge / blood vessel development / central nervous system neuron development / Detoxification of Reactive Oxygen Species / cuprous ion binding / Ion transport by P-type ATPases / microvillus / positive regulation of cell size / intracellular copper ion homeostasis / blood vessel remodeling / positive regulation of lamellipodium assembly / cellular response to copper ion / cellular response to cadmium ion / lactation / removal of superoxide radicals / mitochondrion organization / extracellular matrix organization / neuron projection morphogenesis / trans-Golgi network membrane / liver development / secretory granule / locomotory behavior / positive regulation of epithelial cell proliferation / female pregnancy / cellular response to iron ion / brush border membrane / cellular response to amino acid stimulus / trans-Golgi network / small GTPase binding / phagocytic vesicle membrane / late endosome / early endosome membrane / protein-folding chaperone binding / cellular response to hypoxia / basolateral plasma membrane / perikaryon / in utero embryonic development / postsynaptic density / neuron projection / apical plasma membrane / copper ion binding / axon / neuronal cell body / dendrite / perinuclear region of cytoplasm / Golgi apparatus / endoplasmic reticulum / ATP hydrolysis activity / ATP binding / membrane / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION NMR / simulated annealing | ||||||
Authors | De Silva, T.M. / Veglia, G. / Opella, S.J. | ||||||
Citation | Journal: Proteins / Year: 2005 Title: Solution structures of the reduced and Cu(I) bound forms of the first metal binding sequence of ATP7A associated with Menkes disease. Authors: DeSilva, T.M. / Veglia, G. / Opella, S.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1kvi.cif.gz | 239.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1kvi.ent.gz | 197.2 KB | Display | PDB format |
PDBx/mmJSON format | 1kvi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1kvi_validation.pdf.gz | 343.3 KB | Display | wwPDB validaton report |
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Full document | 1kvi_full_validation.pdf.gz | 458.1 KB | Display | |
Data in XML | 1kvi_validation.xml.gz | 24.5 KB | Display | |
Data in CIF | 1kvi_validation.cif.gz | 35.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kv/1kvi ftp://data.pdbj.org/pub/pdb/validation_reports/kv/1kvi | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 8691.849 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-79 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pMAl / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21DE3 / References: UniProt: Q04656, Cu2+-exporting ATPase |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR |
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-Sample preparation
Details | Contents: 20 mM NaAcetate buffer, 10 mM DTT, 1 mM EDTA, 0.01% Na Azide, 1 mM Protein Solvent system: H2O/D2O |
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Sample conditions | pH: 6.5 / Pressure: 1 atm / Temperature: 298 K |
Crystal grow | *PLUS Method: other / Details: NMR |
-NMR measurement
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M |
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Radiation wavelength | Relative weight: 1 |
NMR spectrometer | Type: Bruker DMX / Manufacturer: Bruker / Model: DMX / Field strength: 600 MHz |
-Processing
NMR software |
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Refinement | Method: simulated annealing / Software ordinal: 1 | |||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 50 / Conformers submitted total number: 10 |