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Yorodumi- PDB-6cjf: Human dihydroorotate dehydrogenase bound to 4-quinoline carboxyli... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6cjf | ||||||
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Title | Human dihydroorotate dehydrogenase bound to 4-quinoline carboxylic acid inhibitor 43 | ||||||
Components | Dihydroorotate dehydrogenase (quinone), mitochondrialDihydroorotate dehydrogenase (quinone) | ||||||
Keywords | OXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / Oxidoreductase / oxidoreductase inhibitor / 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: 1.63 Å | ||||||
Authors | Petrunak, E.M. / Stuckey, J.A. | ||||||
Citation | Journal: J. Med. Chem. / Year: 2018 Title: Design, Synthesis, and Biological Evaluation of 4-Quinoline Carboxylic Acids as Inhibitors of Dihydroorotate Dehydrogenase. Authors: Madak, J.T. / Cuthbertson, C.R. / Miyata, Y. / Tamura, S. / Petrunak, E.M. / Stuckey, J.A. / Han, Y. / He, M. / Sun, D. / Showalter, H.D. / Neamati, N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6cjf.cif.gz | 161.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6cjf.ent.gz | 122.8 KB | Display | PDB format |
PDBx/mmJSON format | 6cjf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cj/6cjf ftp://data.pdbj.org/pub/pdb/validation_reports/cj/6cjf | HTTPS FTP |
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-Related structure data
Related structure data | 6cjgC 4ighS 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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2 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 40752.434 Da / Num. of mol.: 2 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, 374 molecules
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
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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: 2.01 Å3/Da / Density % sol: 38.75 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 1.72 M ammonium sulfate, 1.4 M sodium chloride, 0.1 M sodium acetate pH 5.3, 10 mM DTT |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.9786 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 14, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9786 Å / Relative weight: 1 |
Reflection | Resolution: 1.63→50 Å / Num. obs: 75537 / % possible obs: 97.2 % / Redundancy: 4 % / Rsym value: 0.056 / Net I/σ(I): 10 |
Reflection shell | Resolution: 1.63→1.66 Å / Mean I/σ(I) obs: 2 / Rsym value: 0.429 / % possible all: 95.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4IGH Resolution: 1.63→32.473 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 2 / Phase error: 18.6 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.63→32.473 Å
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Refine LS restraints |
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LS refinement shell |
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