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- PDB-4j7u: Crystal structure of human sepiapterin reductase in complex with ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4j7u | ||||||
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Title | Crystal structure of human sepiapterin reductase in complex with sulfathiazole | ||||||
![]() | Sepiapterin reductase | ||||||
![]() | OXIDOREDUCTASE/ANTIBIOTIC / Reductase / OXIDOREDUCTASE-ANTIBIOTIC complex | ||||||
Function / homology | ![]() sepiapterin reductase (L-erythro-7,8-dihydrobiopterin forming) / sepiapterin reductase (NADP+) activity / aldo-keto reductase (NADPH) activity / tetrahydrobiopterin biosynthetic process / eNOS activation / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / nitric oxide biosynthetic process / NADP binding / extracellular exosome / nucleoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Groenlund Pedersen, M. / Pojer, F. / Johnsson, K. | ||||||
![]() | ![]() Title: Tetrahydrobiopterin biosynthesis as an off-target of sulfa drugs. Authors: Haruki, H. / Pedersen, M.G. / Gorska, K.I. / Pojer, F. / Johnsson, K. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 213.8 KB | Display | ![]() |
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PDB format | ![]() | 171.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.8 MB | Display | ![]() |
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Full document | ![]() | 2.9 MB | Display | |
Data in XML | ![]() | 40.1 KB | Display | |
Data in CIF | ![]() | 53.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4hwkSC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: GLY / End label comp-ID: GLY / Refine code: 4 / Auth seq-ID: 5 - 250 / Label seq-ID: 35 - 280
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Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 31290.029 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P35270, sepiapterin reductase (L-erythro-7,8-dihydrobiopterin forming) |
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-Non-polymers , 6 types, 169 molecules ![](data/chem/img/NAP.gif)
![](data/chem/img/YTZ.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/YTZ.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-NAP / #3: Chemical | ChemComp-YTZ / #4: Chemical | ChemComp-SO4 / #5: Chemical | ChemComp-PEG / #6: Chemical | #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.52 Å3/Da / Density % sol: 72.79 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 1.70 M ammonium sulphate, 0.1 M HEPES, 2 % w/v PEG 1000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Nov 2, 2011 |
Radiation | Monochromator: Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.45→50 Å / Num. all: 162423 / Num. obs: 161097 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 2.45→2.59 Å / % possible all: 95.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4HWK Resolution: 2.44→48.37 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.93 / SU B: 6.061 / SU ML: 0.138 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.212 / ESU R Free: 0.185 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 41.908 Å2
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Refinement step | Cycle: LAST / Resolution: 2.44→48.37 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Ens-ID: 1 / Number: 1848 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 2.443→2.507 Å / Total num. of bins used: 20
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