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Yorodumi- PDB-3kvk: Crystal structure of human dihydroorotate dehydrogenase (DHODH) w... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3kvk | ||||||
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Title | Crystal structure of human dihydroorotate dehydrogenase (DHODH) with amino-benzoic acid inhibitor 641 at 2.05A resolution | ||||||
Components | Dihydroorotate dehydrogenase, mitochondrial | ||||||
Keywords | OXIDOREDUCTASE / PROTEIN-ANTIPROLIFERATIVE AGENT COMPLEX / Flavoprotein / FMN / Membrane / Mitochondrion / Mitochondrion inner membrane / Polymorphism / Pyrimidine biosynthesis / Transit peptide / Transmembrane | ||||||
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 / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.05 Å | ||||||
Authors | McLean, L. / Zhang, Y. | ||||||
Citation | Journal: Bioorg.Med.Chem.Lett. / Year: 2010 Title: Discovery of novel inhibitors for DHODH via virtual screening and X-ray crystallographic structures. Authors: McLean, L.R. / Zhang, Y. / Degnen, W. / Peppard, J. / Cabel, D. / Zou, C. / Tsay, J.T. / Subramaniam, A. / Vaz, R.J. / Li, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3kvk.cif.gz | 94.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3kvk.ent.gz | 68.1 KB | Display | PDB format |
PDBx/mmJSON format | 3kvk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kv/3kvk ftp://data.pdbj.org/pub/pdb/validation_reports/kv/3kvk | HTTPS FTP |
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-Related structure data
Related structure data | 3kvjC 3kvlC 3kvmC 1d3gS C: citing same article (ref.) 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 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, 239 molecules
#2: Chemical | ChemComp-SO4 / |
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#3: Chemical | ChemComp-FMN / |
#4: Chemical | ChemComp-DOR / ( |
#5: Chemical | ChemComp-DET / |
#6: Chemical | ChemComp-6X1 / |
#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: 3.44 Å3/Da / Density % sol: 64.28 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 2.4 M AMMONIUM SULFATE, 15% GLYCEROL, 0.1 M NA-ACETATE, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Oct 16, 2006 / Details: XENOCS FOX 2D | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.05→50 Å / Num. obs: 37082 / % possible obs: 98.8 % / Redundancy: 9.6 % / Rmerge(I) obs: 0.164 / Χ2: 1.001 / Net I/σ(I): 6.6 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1D3G Resolution: 2.05→36.56 Å / Rfactor Rfree error: 0.005 / Occupancy max: 1 / Occupancy min: 0.5 / Data cutoff high absF: 309643 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 62.124 Å2 / ksol: 0.392 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 77.73 Å2 / Biso mean: 28.656 Å2 / Biso min: 10.93 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.05→36.56 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.05→2.18 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
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Xplor file |
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