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- PDB-6de4: Homo sapiens dihydrofolate reductase complexed with beta-NADPH an... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6de4 | ||||||
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Title | Homo sapiens dihydrofolate reductase complexed with beta-NADPH and 3'-[(2R)-4-(2,4-diamino-6-ethylphenyl)but-3-yn-2-yl]-5'-methoxy-[1,1'-biphenyl]-4-carboxylic acid | ||||||
![]() | Dihydrofolate reductase | ||||||
![]() | oxidoreductase/oxidoreductase inhibitor / DHFR / Antifolates / oxidoreductase-oxidoreductase inhibitor complex | ||||||
Function / homology | ![]() regulation of removal of superoxide radicals / tetrahydrobiopterin biosynthetic process / Metabolism of folate and pterines / tetrahydrofolate metabolic process / sequence-specific mRNA binding / response to methotrexate / axon regeneration / folic acid binding / G1/S-Specific Transcription / dihydrofolate metabolic process ...regulation of removal of superoxide radicals / tetrahydrobiopterin biosynthetic process / Metabolism of folate and pterines / tetrahydrofolate metabolic process / sequence-specific mRNA binding / response to methotrexate / axon regeneration / folic acid binding / G1/S-Specific Transcription / dihydrofolate metabolic process / glycine biosynthetic process / dihydrofolate reductase / dihydrofolate reductase activity / folic acid metabolic process / NADPH binding / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / tetrahydrofolate biosynthetic process / mRNA regulatory element binding translation repressor activity / positive regulation of nitric-oxide synthase activity / one-carbon metabolic process / NADP binding / negative regulation of translation / mRNA binding / mitochondrion / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Hajian, B. / Wright, D. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Drugging the Folate Pathway in Mycobacterium tuberculosis: The Role of Multi-targeting Agents. Authors: Hajian, B. / Scocchera, E. / Shoen, C. / Krucinska, J. / Viswanathan, K. / G-Dayanandan, N. / Erlandsen, H. / Estrada, A. / Mikusova, K. / Kordulakova, J. / Cynamon, M. / Wright, D. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 101.2 KB | Display | ![]() |
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PDB format | ![]() | 77.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.7 MB | Display | ![]() |
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Full document | ![]() | 1.7 MB | Display | |
Data in XML | ![]() | 19.6 KB | Display | |
Data in CIF | ![]() | 25 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6ddpC ![]() 6ddsC ![]() 6ddwC ![]() 6de5C ![]() 4kakS 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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Components on special symmetry positions |
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 21349.525 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 8 types, 86 molecules ![](data/chem/img/NDP.gif)
![](data/chem/img/G6Y.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/EOH.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/G6Y.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/EOH.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | #6: Chemical | ChemComp-EOH / #7: Chemical | #8: Chemical | #9: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.63 Å3/Da / Density % sol: 73.41 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion Details: 0.1M Tris Ph 7.6,0.2M LiSo4, 15mM CaCl2, 6% EtOH, 15% Ethylene glycol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 24, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.411→42.364 Å / Num. obs: 30735 / % possible obs: 99.45 % / Redundancy: 7.7 % / Rpim(I) all: 0.082 / Rsym value: 0.082 / Net I/σ(I): 7.4 |
Reflection shell | Resolution: 2.41→2.45 Å / Rpim(I) all: 0.779 / Rsym value: 0.779 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4KAK Resolution: 2.411→42.364 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 21.99
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.411→42.364 Å
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Refine LS restraints |
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LS refinement shell |
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