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Yorodumi- PDB-5zfb: Structure of human dihydroorotate dehydrogenase in complex with a... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5zfb | ||||||
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Title | Structure of human dihydroorotate dehydrogenase in complex with ascofuranone (open-form) | ||||||
Components | Dihydroorotate dehydrogenase (quinone), mitochondrial | ||||||
Keywords | OXIDOREDUCTASE / ROSSMANN FOLD / DIHYDROOROTATE/OROTATE / UBIQUINONE/UBIQUINOL / MITOCHONDRIAL INNER MEMBRANE / INHIBITOR COMPLEX | ||||||
Function / homology | Function and homology information 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 / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Miyazaki, Y. / Inaoka, K.D. / Shiba, T. / Saimoto, H. / Amalia, E. / Kido, Y. / Sakai, C. / Nakamura, M. / Moore, L.A. / Harada, S. / Kita, K. | ||||||
Citation | Journal: Front Pharmacol / Year: 2018 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5zfb.cif.gz | 96.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5zfb.ent.gz | 69.9 KB | Display | PDB format |
PDBx/mmJSON format | 5zfb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5zfb_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 5zfb_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 5zfb_validation.xml.gz | 18.4 KB | Display | |
Data in CIF | 5zfb_validation.cif.gz | 26.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zf/5zfb ftp://data.pdbj.org/pub/pdb/validation_reports/zf/5zfb | HTTPS FTP |
-Related structure data
Related structure data | 5zf4C 5zf7C 5zf8C 5zf9C 5zfaC 3zwsS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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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.) Homo sapiens (human) / Gene: DHODH / Plasmid: PET19B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)PYRD References: UniProt: Q02127, dihydroorotate dehydrogenase (quinone) |
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-Non-polymers , 6 types, 193 molecules
#2: Chemical | ChemComp-FMN / | ||||
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#3: Chemical | ChemComp-ORO / | ||||
#4: Chemical | ChemComp-ACT / | ||||
#5: Chemical | ChemComp-SO4 / #6: Chemical | ChemComp-9BX / | #7: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.42 Å3/Da / Density % sol: 64 % |
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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: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å |
Detector | Type: RAYONIX MX-225 / Detector: CCD / Date: Jan 24, 2011 |
Radiation | Monochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. obs: 39966 / % possible obs: 99.3 % / Redundancy: 6 % / Rmerge(I) obs: 0.097 / Net I/σ(I): 10.4 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 5.2 / Num. unique obs: 3947 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3ZWS Resolution: 2→29.57 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.943 / SU B: 2.415 / SU ML: 0.068 / Cross valid method: THROUGHOUT / ESU R: 0.119 / ESU R Free: 0.112 / 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: 25.153 Å2
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Refinement step | Cycle: 1 / Resolution: 2→29.57 Å
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