+Open data
-Basic information
Entry | Database: PDB / ID: 6j3b | ||||||
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Title | Crystal structure of human DHODH in complex with inhibitor 1289 | ||||||
Components | Dihydroorotate dehydrogenase (quinone), mitochondrialDihydroorotate dehydrogenase (quinone) | ||||||
Keywords | OXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / DHODH / Inhibitor / Complex / 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 / Resolution: 1.6 Å | ||||||
Authors | Yu, Y. / Chen, Q. | ||||||
Citation | Journal: Febs Open Bio / Year: 2019 Title: A novel series of human dihydroorotate dehydrogenase inhibitors discovered by in vitro screening: inhibition activity and crystallographic binding mode. Authors: Zeng, T. / Zuo, Z. / Luo, Y. / Zhao, Y. / Yu, Y. / Chen, Q. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6j3b.cif.gz | 167.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6j3b.ent.gz | 131.4 KB | Display | PDB format |
PDBx/mmJSON format | 6j3b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j3/6j3b ftp://data.pdbj.org/pub/pdb/validation_reports/j3/6j3b | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 39725.344 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 , 10 types, 349 molecules
#2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-FMN / | #4: Chemical | ChemComp-ORO / | #5: Chemical | ChemComp-B5O / ( | #6: Chemical | ChemComp-LDA / | #7: Chemical | #8: Chemical | ChemComp-ACT / #9: Chemical | #10: Chemical | #11: 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: 3.68 Å3/Da / Density % sol: 66.57 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: HEPES pH4.6, 2M AMMONIUM SULPHATE, 30% Glycerol / PH range: 4.6 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.979 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 28, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→50 Å / Num. obs: 77757 / % possible obs: 100 % / Redundancy: 10 % / Rpim(I) all: 0.056 / Net I/σ(I): 13.6 |
Reflection shell | Resolution: 1.6→1.63 Å / Num. unique obs: 3842 / Rpim(I) all: 0.248 |
-Processing
Software |
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Refinement | Resolution: 1.6→48.389 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 16.35
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.6→48.389 Å
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Refine LS restraints |
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LS refinement shell |
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