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- PDB-5zf8: Structure of human dihydroorotate dehydrogenase in complex with 2... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5zf8 | ||||||
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Title | Structure of human dihydroorotate dehydrogenase in complex with 277-11-OAc | ||||||
![]() | Dihydroorotate dehydrogenase (quinone), mitochondrial | ||||||
![]() | OXIDOREDUCTASE / ROSSMANN FOLD / DIHYDROOROTATE/OROTATE / UBIQUINONE/UBIQUINOL / MITOCHONDRIAL INNER MEMBRANE / INHIBITOR COMPLEX | ||||||
Function / homology | ![]() pyrimidine ribonucleotide biosynthetic process / dihydroorotate dehydrogenase (quinone) activity / dihydroorotate dehydrogenase (quinone) / dihydroorotate dehydrogenase activity / dihydroorotase activity / Pyrimidine biosynthesis / UDP biosynthetic process / 'de novo' UMP biosynthetic process / 'de novo' pyrimidine nucleobase biosynthetic process / mitochondrial inner membrane ...pyrimidine ribonucleotide biosynthetic process / dihydroorotate dehydrogenase (quinone) activity / dihydroorotate dehydrogenase (quinone) / dihydroorotate dehydrogenase activity / dihydroorotase activity / Pyrimidine biosynthesis / UDP biosynthetic process / 'de novo' UMP biosynthetic process / 'de novo' pyrimidine nucleobase biosynthetic process / mitochondrial inner membrane / mitochondrion / nucleoplasm / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Miyazaki, Y. / Inaoka, K.D. / Shiba, T. / Saimoto, H. / Amalia, E. / Kido, Y. / Sakai, C. / Nakamura, M. / Moore, L.A. / Harada, S. / Kita, K. | ||||||
![]() | ![]() Title: Selective Cytotoxicity of Dihydroorotate Dehydrogenase Inhibitors to Human Cancer Cells Under Hypoxia and Nutrient-Deprived Conditions. Authors: Miyazaki, Y. / Inaoka, D.K. / Shiba, T. / Saimoto, H. / Sakura, T. / Amalia, E. / Kido, Y. / Sakai, C. / Nakamura, M. / Moore, A.L. / Harada, S. / Kita, K. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 97.5 KB | Display | ![]() |
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PDB format | ![]() | 70.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 18.3 KB | Display | |
Data in CIF | ![]() | 26.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5zf4C ![]() 5zf7C ![]() 5zf9C ![]() 5zfaC ![]() 5zfbC ![]() 3zwsS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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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, 1 molecules A
#1: Protein | Mass: 42636.414 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q02127, dihydroorotate dehydrogenase (quinone) |
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-Non-polymers , 6 types, 246 molecules ![](data/chem/img/FMN.gif)
![](data/chem/img/ORO.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/9BO.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/ORO.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/9BO.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-FMN / | ||||||
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#3: Chemical | ChemComp-ORO / | ||||||
#4: Chemical | ChemComp-ACT / #5: Chemical | #6: Chemical | ChemComp-9BO / ( | #7: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.4 Å3/Da / Density % sol: 63.82 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.9 Details: 100MM SODIUM ACETATE, 1.8-1.9M AMMONIUM SULPHATE, 40MM C11DAO, 20.8MM DDAO, 2MM DIHYDROOROTATE |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: May 2, 2011 |
Radiation | Monochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→50 Å / Num. obs: 64294 / % possible obs: 100 % / Redundancy: 10.6 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 13 |
Reflection shell | Resolution: 1.7→1.73 Å / Mean I/σ(I) obs: 4.9 / Num. unique obs: 3157 / Rsym value: 0.566 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3ZWS Resolution: 1.7→33.02 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.961 / SU B: 1.29 / SU ML: 0.043 / Cross valid method: THROUGHOUT / ESU R: 0.075 / ESU R Free: 0.072 / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.988 Å2
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Refinement step | Cycle: 1 / Resolution: 1.7→33.02 Å
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Refine LS restraints |
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