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Open data
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Basic information
Entry | Database: PDB / ID: 5uio | ||||||
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Title | structure of DHFR with bound DAP, p-ABG and NADP | ||||||
![]() | Dihydrofolate reductase | ||||||
![]() | OXIDOREDUCTASE / DHFR / NADP / 2 / 4 diaminopyridine / N-(4aminobenzoyl)-L-glutamate | ||||||
Function / homology | ![]() methotrexate binding / dihydrofolic acid binding / response to methotrexate / NADP+ binding / folic acid binding / dihydrofolate metabolic process / glycine biosynthetic process / dihydrofolate reductase / dihydrofolate reductase activity / folic acid metabolic process ...methotrexate binding / dihydrofolic acid binding / response to methotrexate / NADP+ binding / folic acid binding / dihydrofolate metabolic process / glycine biosynthetic process / dihydrofolate reductase / dihydrofolate reductase activity / folic acid metabolic process / NADPH binding / tetrahydrofolate biosynthetic process / one-carbon metabolic process / NADP binding / response to xenobiotic stimulus / response to antibiotic / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Pedersen, L.C. / London, R.E. | ||||||
![]() | ![]() Title: A Structural Basis for Biguanide Activity. Authors: Gabel, S.A. / Duff, M.R. / Pedersen, L.C. / DeRose, E.F. / Krahn, J.M. / Howell, E.E. / London, R.E. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 192.5 KB | Display | ![]() |
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PDB format | ![]() | 154.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.6 MB | Display | ![]() |
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Full document | ![]() | 2.6 MB | Display | |
Data in XML | ![]() | 39.7 KB | Display | |
Data in CIF | ![]() | 54.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5uihC ![]() 5uiiC ![]() 5uipC ![]() 1ra3S C: citing same article ( S: Starting model for refinement |
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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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3 | ![]()
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4 | ![]()
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5 | ![]()
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Unit cell |
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Components
-Protein , 1 types, 5 molecules ABCDE
#1: Protein | Mass: 19207.625 Da / Num. of mol.: 5 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Non-polymers , 6 types, 635 molecules ![](data/chem/img/LG3.gif)
![](data/chem/img/8DM.gif)
![](data/chem/img/NAP.gif)
![](data/chem/img/BME.gif)
![](data/chem/img/FMT.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/8DM.gif)
![](data/chem/img/NAP.gif)
![](data/chem/img/BME.gif)
![](data/chem/img/FMT.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-LG3 / #3: Chemical | ChemComp-8DM / #4: Chemical | ChemComp-NAP / #5: Chemical | ChemComp-BME / #6: Chemical | #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.47 Å3/Da / Density % sol: 50.2 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 2mM NADP,10mM DAP,50mM p-ABP,0.2M Magnesium Formate,20% PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU SATURN 944+ / Detector: CCD / Date: Jun 16, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 1.93→50 Å / Num. obs: 72439 / % possible obs: 100 % / Redundancy: 7.9 % / Rsym value: 0.058 / Net I/σ(I): 18.6 |
Reflection shell | Resolution: 1.93→1.96 Å / Redundancy: 4.3 % / Mean I/σ(I) obs: 2.7 / Num. unique obs: 3616 / Rsym value: 0.475 / % possible all: 99.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1RA3 Resolution: 1.929→35.446 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 22.78 / 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: 1.929→35.446 Å
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Refine LS restraints |
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LS refinement shell |
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