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- PDB-1d3h: HUMAN DIHYDROOROTATE DEHYDROGENASE COMPLEXED WITH ANTIPROLIFERATI... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1d3h | ||||||
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Title | HUMAN DIHYDROOROTATE DEHYDROGENASE COMPLEXED WITH ANTIPROLIFERATIVE AGENT A771726 | ||||||
![]() | DIHYDROOROTATE DEHYDROGENASE | ||||||
![]() | OXIDOREDUCTASE / ALPHA-BETA BARREL / MEMBRANE BINDING MOTIF | ||||||
Function / homology | ![]() 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 / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Liu, S. / Neidhardt, E.A. / Grossman, T.H. / Ocain, T. / Clardy, J. | ||||||
![]() | ![]() Title: Structures of human dihydroorotate dehydrogenase in complex with antiproliferative agents. Authors: Liu, S. / Neidhardt, E.A. / Grossman, T.H. / Ocain, T. / Clardy, J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 92.4 KB | Display | ![]() |
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PDB format | ![]() | 69.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1 MB | Display | ![]() |
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Full document | ![]() | 1 MB | Display | |
Data in XML | ![]() | 19.7 KB | Display | |
Data in CIF | ![]() | 29.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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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: 39856.535 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 6 types, 303 molecules ![](data/chem/img/SO4.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/A26.gif)
![](data/chem/img/FMN.gif)
![](data/chem/img/ORO.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/A26.gif)
![](data/chem/img/FMN.gif)
![](data/chem/img/ORO.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-SO4 / |
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#3: Chemical | ChemComp-ACT / |
#4: Chemical | ChemComp-A26 / ( |
#5: Chemical | ChemComp-FMN / |
#6: Chemical | ChemComp-ORO / |
#7: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.64 Å3/Da / Density % sol: 66.19 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion Details: ammonium sulphate, acetate buffer, glycerol, DDAO, C11DAO, A771726, orotate, VAPOR DIFFUSION, temperature 293K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: May 5, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9134 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→23.5 Å / Num. all: 55112 / Num. obs: 54515 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.9 % / Biso Wilson estimate: 15.7 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 16.1 |
Reflection shell | Resolution: 1.8→1.9 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.205 / Num. unique all: 7943 / % possible all: 100 |
Reflection | *PLUS % possible obs: 99 % / Num. measured all: 264642 / Rmerge(I) obs: 0.079 |
Reflection shell | *PLUS % possible obs: 99.8 % / Rmerge(I) obs: 0.204 |
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Processing
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Refinement | Resolution: 1.8→30 Å / Rfactor Rfree error: 0.004 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: Used weighted least squares procedure.
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 63.87 Å2 / ksol: 0.428 e/Å3 | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.8→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.91 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 0.5 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 0 / % reflection Rfree: 5 % | ||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 21.6 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.207 / % reflection Rfree: 5.2 % / Rfactor Rwork: 0.176 / Rfactor obs: 0.176 |