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- PDB-7mx6: Leishmania major dihydroorotate dehydrogenase in complex with [4-... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7mx6 | ||||||
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Title | Leishmania major dihydroorotate dehydrogenase in complex with [4-(1H-pyrrol-1-yl)phenyl]methanol | ||||||
![]() | Dihydroorotate dehydrogenase (fumarate) | ||||||
![]() | OXIDOREDUCTASE / Leishmania major / neglected tropical disease / dihydroorotate dehydrogenase | ||||||
Function / homology | ![]() dihydroorotate dehydrogenase (fumarate) / dihydroorotate dehydrogenase (fumarate) activity / fumarate metabolic process / dihydroorotate dehydrogenase activity / ciliary plasm / 'de novo' UMP biosynthetic process / 'de novo' pyrimidine nucleobase biosynthetic process / nucleotide binding / nucleoplasm / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Pinheiro, M.P. / Hunter, W.N. / Cardoso, I.A. / Nonato, M.C. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Leishmania major dihydroorotate dehydrogenase in complex with [4-(1H-pyrrol-1-yl)phenyl]methanol Authors: Pinheiro, M.P. / Hunter, W.N. / Cardoso, I.A. / Nonato, M.C. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 256.2 KB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.3 MB | Display | ![]() |
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Full document | ![]() | 1.3 MB | Display | |
Data in XML | ![]() | 27.7 KB | Display | |
Data in CIF | ![]() | 40.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3gyeS S: Starting model for refinement |
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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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Unit cell |
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Components
-Protein , 1 types, 2 molecules AAABBB
#1: Protein | Mass: 34779.797 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q4QEW7, dihydroorotate dehydrogenase (fumarate) |
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-Non-polymers , 5 types, 395 molecules ![](data/chem/img/FMN.gif)
![](data/chem/img/SNU.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/SNU.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | ChemComp-SNU / | #4: Chemical | ChemComp-SO4 / #5: Chemical | ChemComp-GOL / #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: 2.88 Å3/Da / Density % sol: 57.35 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop Details: 100 mM sodium citrate tribasic dihydrate, pH 5.6, 1.3 M lithium sulfate, 0.30 M ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Feb 28, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.437 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→35.24 Å / Num. obs: 73441 / % possible obs: 100 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.085 / Rsym value: 0.085 / Net I/σ(I): 14.8 |
Reflection shell | Resolution: 1.8→1.9 Å / Redundancy: 6 % / Rmerge(I) obs: 0.704 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 10637 / Rsym value: 0.704 / % possible all: 98.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 3GYE Resolution: 1.8→35.24 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.954 / SU B: 2.106 / SU ML: 0.064 / Cross valid method: FREE R-VALUE / ESU R: 0.098 / ESU R Free: 0.093 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: 20.497 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→35.24 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
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