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Yorodumi- PDB-4a7g: Structure of human I113T SOD1 mutant complexed with 4-methylpiper... -
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-Basic information
Entry | Database: PDB / ID: 4a7g | ||||||
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Title | Structure of human I113T SOD1 mutant complexed with 4-methylpiperazin- 1-yl)quinazoline in the p21 space group. | ||||||
Components | (SUPEROXIDE DISMUTASE [CU- ...) x 2 | ||||||
Keywords | OXIDOREDUCTASE / AMYOTROPHIC LATERAL SCLEROSIS / ANTIOXIDANT / DISEASE MUTATION / METAL-BINDING / ZN SUPEROXIDE DISMUTASE | ||||||
Function / homology | Function and homology information action potential initiation / neurofilament cytoskeleton organization / anterograde axonal transport / retrograde axonal transport / positive regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / protein phosphatase 2B binding / regulation of organ growth / relaxation of vascular associated smooth muscle / response to superoxide / peripheral nervous system myelin maintenance ...action potential initiation / neurofilament cytoskeleton organization / anterograde axonal transport / retrograde axonal transport / positive regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / protein phosphatase 2B binding / regulation of organ growth / relaxation of vascular associated smooth muscle / response to superoxide / peripheral nervous system myelin maintenance / regulation of T cell differentiation in thymus / superoxide anion generation / retina homeostasis / negative regulation of cholesterol biosynthetic process / hydrogen peroxide biosynthetic process / auditory receptor cell stereocilium organization / regulation of protein kinase activity / myeloid cell homeostasis / muscle cell cellular homeostasis / regulation of GTPase activity / superoxide metabolic process / heart contraction / positive regulation of catalytic activity / superoxide dismutase / Detoxification of Reactive Oxygen Species / transmission of nerve impulse / negative regulation of reproductive process / negative regulation of developmental process / superoxide dismutase activity / neuronal action potential / regulation of multicellular organism growth / response to axon injury / ectopic germ cell programmed cell death / glutathione metabolic process / positive regulation of phagocytosis / ovarian follicle development / axon cytoplasm / embryo implantation / reactive oxygen species metabolic process / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / dendrite cytoplasm / removal of superoxide radicals / positive regulation of superoxide anion generation / regulation of mitochondrial membrane potential / thymus development / locomotory behavior / placenta development / response to organic substance / determination of adult lifespan / positive regulation of cytokine production / sensory perception of sound / response to hydrogen peroxide / mitochondrial intermembrane space / small GTPase binding / regulation of blood pressure / negative regulation of inflammatory response / peroxisome / Platelet degranulation / gene expression / response to heat / protein-folding chaperone binding / cytoplasmic vesicle / spermatogenesis / response to ethanol / intracellular iron ion homeostasis / negative regulation of neuron apoptotic process / positive regulation of MAPK cascade / mitochondrial matrix / response to xenobiotic stimulus / positive regulation of apoptotic process / copper ion binding / neuronal cell body / apoptotic process / protein-containing complex / mitochondrion / extracellular space / extracellular exosome / zinc ion binding / extracellular region / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 1.24 Å | ||||||
Authors | Wright, G.S.A. / Kershaw, N.M. / Sharma, R. / Antonyuk, S.V. / Strange, R.W. / Berry, N.G. / O'Neil, P.M. / Hasnain, S.S. | ||||||
Citation | Journal: Curr.Med.Chem. / Year: 2013 Title: X-ray crystallography and computational docking for the detection and development of protein-ligand interactions. Authors: Kershaw, N.M. / Wright, G.S. / Sharma, R. / Antonyuk, S.V. / Strange, R.W. / Berry, N.G. / O'Neill, P.M. / Hasnain, S.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4a7g.cif.gz | 149 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4a7g.ent.gz | 124.5 KB | Display | PDB format |
PDBx/mmJSON format | 4a7g.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a7/4a7g ftp://data.pdbj.org/pub/pdb/validation_reports/a7/4a7g | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-SUPEROXIDE DISMUTASE [CU- ... , 2 types, 2 molecules AF
#1: Protein | Mass: 15803.453 Da / Num. of mol.: 1 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PET303 / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / References: UniProt: P00441, superoxide dismutase |
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#2: Protein | Mass: 15815.508 Da / Num. of mol.: 1 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PET303 / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / References: UniProt: P00441, superoxide dismutase |
-Non-polymers , 6 types, 401 molecules
#3: Chemical | ChemComp-SO4 / #4: Chemical | #5: Chemical | #6: Chemical | #7: Chemical | ChemComp-ACT / | #8: Water | ChemComp-HOH / | |
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-Details
Compound details | ENGINEERED |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.9 Å3/Da / Density % sol: 34 % / Description: NONE |
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Crystal grow | pH: 5 Details: 100MM SODIUM ACETATE PH 5, 150 MM SODIUM CHLORIDE, 2.5 M AMMONIUM SULPHATE |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.866 |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 6, 2010 / Details: MIRRORS |
Radiation | Monochromator: SI111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.866 Å / Relative weight: 1 |
Reflection | Resolution: 1.24→50 Å / Num. obs: 71339 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Biso Wilson estimate: 10.4 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 14 |
Reflection shell | Resolution: 1.24→1.28 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.69 / Mean I/σ(I) obs: 1.7 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: OTHER Starting model: NONE Resolution: 1.24→48.33 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.966 / SU B: 1.485 / SU ML: 0.029 / Cross valid method: THROUGHOUT / ESU R: 0.046 / ESU R Free: 0.046 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 12.052 Å2
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Refinement step | Cycle: LAST / Resolution: 1.24→48.33 Å
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