+Open data
-Basic information
Entry | Database: PDB / ID: 6oc0 | ||||||
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Title | Crystal structure of human DHODH with OSU-03012 | ||||||
Components | Dihydroorotate dehydrogenase (quinone), mitochondrialDihydroorotate dehydrogenase (quinone) | ||||||
Keywords | OXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / DHODH / Inhibitor / OSU-03012 / OXIDOREDUCTASE / OXIDOREDUCTASE-OXIDOREDUCTASE 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: 1.4 Å | ||||||
Authors | Durst, M.A. / Lavie, A. | ||||||
Citation | Journal: Cell Chem Biol / Year: 2020 Title: Metabolic Modifier Screen Reveals Secondary Targets of Protein Kinase Inhibitors within Nucleotide Metabolism. Authors: Abt, E.R. / Rosser, E.W. / Durst, M.A. / Lok, V. / Poddar, S. / Le, T.M. / Cho, A. / Kim, W. / Wei, L. / Song, J. / Capri, J.R. / Xu, S. / Wu, N. / Slavik, R. / Jung, M.E. / Damoiseaux, R. / ...Authors: Abt, E.R. / Rosser, E.W. / Durst, M.A. / Lok, V. / Poddar, S. / Le, T.M. / Cho, A. / Kim, W. / Wei, L. / Song, J. / Capri, J.R. / Xu, S. / Wu, N. / Slavik, R. / Jung, M.E. / Damoiseaux, R. / Czernin, J. / Donahue, T.R. / Lavie, A. / Radu, C.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6oc0.cif.gz | 174.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6oc0.ent.gz | 134.5 KB | Display | PDB format |
PDBx/mmJSON format | 6oc0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oc/6oc0 ftp://data.pdbj.org/pub/pdb/validation_reports/oc/6oc0 | HTTPS FTP |
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-Related structure data
Related structure data | 6oc1C 4oqvS 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: 40125.879 Da / Num. of mol.: 1 / Fragment: residues 29-395 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 , 5 types, 238 molecules
#2: Chemical | ChemComp-ORO / | ||||
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#3: Chemical | ChemComp-FMN / | ||||
#4: Chemical | #5: Chemical | ChemComp-M4J / | #6: 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: 3.72 Å3/Da / Density % sol: 66.92 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5 / Details: Ammonium sulfate, glycerol, DHO, DDAO, OSU-03012 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.999873 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Oct 9, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.999873 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→50 Å / Num. obs: 114363 / % possible obs: 99 % / Redundancy: 9.53 % / CC1/2: 0.999 / Rrim(I) all: 0.07 / Net I/σ(I): 19.21 |
Reflection shell | Resolution: 1.4→1.48 Å / Redundancy: 6.52 % / Mean I/σ(I) obs: 2.76 / Num. unique obs: 17418 / CC1/2: 0.878 / Rrim(I) all: 0.545 / % possible all: 94.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4OQV Resolution: 1.4→48.55 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.962 / SU B: 2.594 / SU ML: 0.041 / Cross valid method: THROUGHOUT / ESU R: 0.044 / ESU R Free: 0.046 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.869 Å2
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Refinement step | Cycle: 1 / Resolution: 1.4→48.55 Å
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Refine LS restraints |
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