+Open data
-Basic information
Entry | Database: PDB / ID: 6syp | ||||||
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Title | Human DHODH bound to inhibitor IPP/CNRS-A017 | ||||||
Components | Dihydroorotate dehydrogenase | ||||||
Keywords | OXIDOREDUCTASE / Dihydroorotate dehydrogenase Inhibitor Complex / Structural Genomics / Structural Genomics Consortium / SGC | ||||||
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: 1.8 Å | ||||||
Authors | Kraemer, A. / Janin, Y. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Knapp, S. / Structural Genomics Consortium (SGC) | ||||||
Citation | Journal: Eur.J.Med.Chem. / Year: 2020 Title: Optimization of pyrazolo[1,5-a]pyrimidines lead to the identification of a highly selective casein kinase 2 inhibitor Authors: Kramer, A. / Kurz, C.G. / Berger, B.T. / Celik, I.E. / Tjaden, A. / Greco, F.A. / Knapp, S. / Hanke, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6syp.cif.gz | 90.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6syp.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 6syp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sy/6syp ftp://data.pdbj.org/pub/pdb/validation_reports/sy/6syp | HTTPS FTP |
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-Related structure data
Related structure data | 5mutS S: Starting model for refinement |
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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 AAA
#1: Protein | Mass: 42929.203 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pFN2A / Production host: Escherichia coli (E. coli) References: UniProt: Q02127, dihydroorotate dehydrogenase (quinone) |
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-Non-polymers , 5 types, 150 molecules
#2: Chemical | ChemComp-FMN / |
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#3: Chemical | ChemComp-ORO / |
#4: Chemical | ChemComp-SO4 / |
#5: Chemical | ChemComp-M0B / |
#6: Water | ChemComp-HOH / |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.38 Å3/Da / Density % sol: 63.56 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.8 / Details: 32% PEG 400 0.2M KSCN 0.2M NaBr 0.1M acetate 4.8 / PH range: 4.8 - 5.2 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.999987 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 5, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.999987 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→48.293 Å / Num. obs: 54364 / % possible obs: 100 % / Redundancy: 9 % / CC1/2: 0.999 / Net I/σ(I): 17.6 |
Reflection shell | Resolution: 1.8→1.84 Å / Num. unique obs: 3192 / CC1/2: 0.691 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5MUT Resolution: 1.8→48.25 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.953 / SU B: 1.943 / SU ML: 0.059 / Cross valid method: FREE R-VALUE / ESU R: 0.088 / ESU R Free: 0.087 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.245 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→48.25 Å
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Refine LS restraints |
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LS refinement shell |
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