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Open data
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Basic information
Entry | Database: PDB / ID: 7t8f | ||||||
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Title | G93A mutant of human SOD1 bound with Ebselen in P21 space group | ||||||
![]() | Superoxide dismutase [Cu-Zn] | ||||||
![]() | OXIDOREDUCTASE / SOD1 / ALS / Drug discovery | ||||||
Function / homology | ![]() action potential initiation / response to antipsychotic drug / neurofilament cytoskeleton organization / response to carbon monoxide / protein phosphatase 2B binding / dense core granule / regulation of organ growth / relaxation of vascular associated smooth muscle / anterograde axonal transport / positive regulation of oxidative stress-induced intrinsic apoptotic signaling pathway ...action potential initiation / response to antipsychotic drug / neurofilament cytoskeleton organization / response to carbon monoxide / protein phosphatase 2B binding / dense core granule / regulation of organ growth / relaxation of vascular associated smooth muscle / anterograde axonal transport / positive regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / response to superoxide / regulation of T cell differentiation in thymus / peripheral nervous system myelin maintenance / retina homeostasis / auditory receptor cell stereocilium organization / hydrogen peroxide biosynthetic process / cellular response to potassium ion / retrograde axonal transport / superoxide anion generation / myeloid cell homeostasis / regulation of GTPase activity / response to copper ion / superoxide metabolic process / muscle cell cellular homeostasis / superoxide dismutase / heart contraction / Detoxification of Reactive Oxygen Species / cellular response to ATP / superoxide dismutase activity / negative regulation of reproductive process / negative regulation of developmental process / transmission of nerve impulse / cellular response to cadmium ion / regulation of multicellular organism growth / ectopic germ cell programmed cell death / response to axon injury / neuronal action potential / ovarian follicle development / positive regulation of superoxide anion generation / regulation of mitochondrial membrane potential / axon cytoplasm / glutathione metabolic process / embryo implantation / dendrite cytoplasm / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / removal of superoxide radicals / reactive oxygen species metabolic process / positive regulation of phagocytosis / placenta development / response to amphetamine / thymus development / positive regulation of cytokine production / determination of adult lifespan / locomotory behavior / response to nutrient levels / response to hydrogen peroxide / sensory perception of sound / regulation of blood pressure / mitochondrial intermembrane space / small GTPase binding / negative regulation of inflammatory response / peroxisome / Platelet degranulation / protein-folding chaperone binding / response to heat / cytoplasmic vesicle / response to ethanol / spermatogenesis / gene expression / negative regulation of neuron apoptotic process / intracellular iron ion homeostasis / lysosome / positive regulation of MAPK cascade / positive regulation of apoptotic process / mitochondrial matrix / response to xenobiotic stimulus / copper ion binding / neuronal cell body / apoptotic process / protein homodimerization activity / protein-containing complex / mitochondrion / extracellular space / extracellular exosome / extracellular region / zinc ion binding / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Amporndanai, K. / Hasnain, S.S. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Ebselen analogues delay disease onset and its course in fALS by on-target SOD-1 engagement. Authors: Watanabe, S. / Amporndanai, K. / Awais, R. / Latham, C. / Awais, M. / O'Neill, P.M. / Yamanaka, K. / Hasnain, S.S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 126.5 KB | Display | ![]() |
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PDB format | ![]() | 94.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1 MB | Display | ![]() |
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Full document | ![]() | 1 MB | Display | |
Data in XML | ![]() | 15.9 KB | Display | |
Data in CIF | ![]() | 22.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7t8eC ![]() 7t8gC ![]() 7t8hC ![]() 2wkoS S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: THR / Beg label comp-ID: THR / End auth comp-ID: ALA / End label comp-ID: ALA / Refine code: 1 / Auth seq-ID: 2 - 152 / Label seq-ID: 2 - 152
NCS ensembles : (Details: Local NCS retraints between domains: 1 2) |
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Components
#1: Protein | Mass: 15841.586 Da / Num. of mol.: 2 / Mutation: G93A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-ACT / | #4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | Has protein modification | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.02 Å3/Da / Density % sol: 38.96 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 4.7 Details: 100mM NaOAc pH 4.7, 150mM NaCl, 2.7M ammonium sulphate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Jan 22, 2021 |
Radiation | Monochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→67.99 Å / Num. obs: 49165 / % possible obs: 99.4 % / Redundancy: 3 % / CC1/2: 0.976 / Rmerge(I) obs: 0.109 / Rpim(I) all: 0.104 / Rrim(I) all: 0.151 / Net I/σ(I): 5.4 |
Reflection shell | Resolution: 1.4→1.42 Å / Redundancy: 2 % / Rmerge(I) obs: 0.496 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 2267 / CC1/2: 0.576 / Rpim(I) all: 0.468 / Rrim(I) all: 0.619 / % possible all: 93.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2WKO Resolution: 1.4→48.609 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.938 / SU B: 1.46 / SU ML: 0.057 / Cross valid method: FREE R-VALUE / ESU R: 0.075 / ESU R Free: 0.074 Details: Hydrogens have been added in their riding positions
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 14.357 Å2
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Refinement step | Cycle: LAST / Resolution: 1.4→48.609 Å
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Refine LS restraints |
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Refine LS restraints NCS |
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LS refinement shell |
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