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Yorodumi- PDB-6gk0: HUMAN DIHYDROOROTATE DEHYDROGENASE IN COMPLEX WITH CLASS III HIST... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6gk0 | ||||||
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Title | HUMAN DIHYDROOROTATE DEHYDROGENASE IN COMPLEX WITH CLASS III HISTONE DEACETYLASE INHIBITOR | ||||||
Components | Dihydroorotate dehydrogenase (quinone), mitochondrialDihydroorotate dehydrogenase (quinone) | ||||||
Keywords | ANTITUMOR PROTEIN / Dehydrogenase DHODH tumor-killing drug development | ||||||
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 / Resolution: 1.85 Å | ||||||
Authors | Hakansson, M. / Ladds, M.J.G.W. / Walse, B. / Lain, S. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2020 Title: Exploitation of dihydroorotate dehydrogenase (DHODH) and p53 activation as therapeutic targets: A case study in polypharmacology. Authors: Ladds, M.J.G.W. / Popova, G. / Pastor-Fernandez, A. / Kannan, S. / van Leeuwen, I.M.M. / Hakansson, M. / Walse, B. / Tholander, F. / Bhatia, R. / Verma, C.S. / Lane, D.P. / Lain, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6gk0.cif.gz | 165.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6gk0.ent.gz | 135.2 KB | Display | PDB format |
PDBx/mmJSON format | 6gk0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gk/6gk0 ftp://data.pdbj.org/pub/pdb/validation_reports/gk/6gk0 | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 39856.535 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: DHODH / Production host: Escherichia coli (E. coli) References: UniProt: Q02127, dihydroorotate dehydrogenase (quinone) |
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-Non-polymers , 9 types, 243 molecules
#2: Chemical | ChemComp-FMN / | ||||||||||||
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#3: Chemical | ChemComp-DOR / ( | ||||||||||||
#4: Chemical | ChemComp-ACY / #5: Chemical | ChemComp-GOL / | #6: Chemical | ChemComp-SO4 / #7: Chemical | ChemComp-CL / | #8: Chemical | ChemComp-DDQ / | #9: Chemical | ChemComp-F1W / | #10: 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: 3.64 Å3/Da / Density % sol: 66.25 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.8 Details: 30% glycerol, 100 mM sodium acetate pH 4.8, 1.8 M Ammoniumsulphate, 40 mM DDAO, 6.4 mM C11DAO, 2 mM L-DHO, 1 mM Tenovin |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: MAX II / Beamline: I911-3 / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 5, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→20 Å / Num. obs: 50141 / % possible obs: 99.8 % / Redundancy: 4.5 % / Net I/σ(I): 5.4 |
Reflection shell | Resolution: 1.85→1.89 Å |
-Processing
Software |
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Refinement | Resolution: 1.85→19.81 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.946 / SU B: 5.548 / SU ML: 0.079 / Cross valid method: THROUGHOUT / ESU R: 0.096 / ESU R Free: 0.095 / Details: HYDROGENS HAVE BEEN ADDED IN THE 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.791 Å2
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Refinement step | Cycle: 1 / Resolution: 1.85→19.81 Å
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Refine LS restraints |
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