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Open data
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Basic information
Entry | Database: PDB / ID: 7t8h | ||||||
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Title | G93A mutant of human SOD1 bound with MR6-26-2 in P21 space group | ||||||
![]() | Superoxide dismutase [Cu-Zn] | ||||||
![]() | ![]() ![]() ![]() ![]() | ||||||
Function / homology | ![]() action potential initiation / neurofilament cytoskeleton organization / 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 / anterograde axonal transport / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() 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 | ![]() | 127.6 KB | Display | ![]() |
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PDB format | ![]() | 95.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 7t8eC ![]() 7t8fC ![]() 7t8gC ![]() 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: ALA / Beg label comp-ID: ALA / End auth comp-ID: GLN / End label comp-ID: GLN / Refine code: 1 / Auth seq-ID: 1 - 153 / Label seq-ID: 1 - 153
NCS ensembles : (Details: Local NCS retraints between domains: 1 2) |
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Components
-Protein , 1 types, 2 molecules AF
#1: Protein | Mass: 15841.586 Da / Num. of mol.: 2 / Mutation: G93A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() |
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-Non-polymers , 5 types, 232 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/Q8E.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/Q8E.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-ACT / | ![]() #4: Chemical | #5: Chemical | ![]() #6: Water | ChemComp-HOH / | ![]() |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.01 Å3/Da / Density % sol: 38.8 % |
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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![]() |
Reflection | Resolution: 1.5→48.303 Å / Num. obs: 40225 / % possible obs: 99.1 % / Redundancy: 2.9 % / CC1/2: 0.994 / Rmerge(I) obs: 0.052 / Rpim(I) all: 0.049 / Rrim(I) all: 0.072 / Net I/σ(I): 9.4 |
Reflection shell | Resolution: 1.5→1.53 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.301 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 1769 / CC1/2: 0.848 / Rpim(I) all: 0.284 / Rrim(I) all: 0.415 / % possible all: 88.6 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 2WKO Resolution: 1.5→48.303 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.94 / SU B: 1.788 / SU ML: 0.064 / Cross valid method: FREE R-VALUE / ESU R: 0.085 / ESU R Free: 0.088 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: 17.367 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→48.303 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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