+Open data
-Basic information
Entry | Database: PDB / ID: 8yhr | ||||||
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Title | DHODH in complex with furocoumavirin | ||||||
Components | Dihydroorotate dehydrogenase (quinone), mitochondrial | ||||||
Keywords | OXIDOREDUCTASE / dihydroorotate dehydrogenase / dhodh / inhibitor | ||||||
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: 1.7 Å | ||||||
Authors | Hara, K. / Okumura, H. / Nakahara, M. / Sato, M. / Hashimoto, H. / Osada, H. / Watanabe, K. | ||||||
Funding support | 1items
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Citation | Journal: Biochemistry / Year: 2024 Title: Structural and Functional Analyses of Inhibition of Human Dihydroorotate Dehydrogenase by Antiviral Furocoumavirin. Authors: Nakahara, M. / Watanabe, S. / Sato, M. / Okumura, H. / Kawatani, M. / Osada, H. / Hara, K. / Hashimoto, H. / Watanabe, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8yhr.cif.gz | 155.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8yhr.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 8yhr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8yhr_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 8yhr_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 8yhr_validation.xml.gz | 18.6 KB | Display | |
Data in CIF | 8yhr_validation.cif.gz | 27.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yh/8yhr ftp://data.pdbj.org/pub/pdb/validation_reports/yh/8yhr | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-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: 42027.879 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 , 7 types, 282 molecules
#2: Chemical | ChemComp-ORO / | ||||||||
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#3: Chemical | ChemComp-FMN / | ||||||||
#4: Chemical | #5: Chemical | ChemComp-ACT / #6: Chemical | ChemComp-SO4 / | #7: Chemical | ChemComp-A1LYU / | Mass: 382.408 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H18O4 / Feature type: SUBJECT OF INVESTIGATION #8: 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: 3.78 Å3/Da / Density % sol: 67.43 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: Sodium acetate (pH 4.8), Ammonium sulfate, Glycerol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 18, 2023 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→36.4 Å / Num. obs: 63419 / % possible obs: 98.57 % / Redundancy: 8.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.0729 / Net I/σ(I): 17.99 |
Reflection shell | Resolution: 1.7→1.761 Å / Num. unique obs: 5673 / CC1/2: 0.875 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→36.395 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 14.51 / 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: 1.7→36.395 Å
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Refine LS restraints |
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LS refinement shell |
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