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- PDB-7zhw: Leishmania donovani Glucose 6-Phosphate Dehydrogenase complexed w... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7zhw | ||||||
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Title | Leishmania donovani Glucose 6-Phosphate Dehydrogenase complexed with NADP(H) and Glucose 6-Phosphate | ||||||
![]() | Glucose-6-phosphate 1-dehydrogenase | ||||||
![]() | OXIDOREDUCTASE / Trypanosoma / Leishmania donovani / Glucose 6-Phosphate Dehydrogenase / G6P / NADP(H) / pentose phosphate pathway | ||||||
Function / homology | ![]() glucose-6-phosphate dehydrogenase (NADP+) / glucose-6-phosphate dehydrogenase activity / pentose-phosphate shunt, oxidative branch / glucose metabolic process / NADP binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Fritz-Wolf, K. / Berneburg, I. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Crystal structure of Leishmania donovani glucose 6-phosphate dehydrogenase reveals a unique N-terminal domain. Authors: Berneburg, I. / Rahlfs, S. / Becker, K. / Fritz-Wolf, 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 | ![]() | 275 KB | Display | ![]() |
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PDB format | ![]() | 180.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.3 MB | Display | ![]() |
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Full document | ![]() | 1.3 MB | Display | |
Data in XML | ![]() | 41 KB | Display | |
Data in CIF | ![]() | 53.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7zhtC ![]() 7zhuC ![]() 7zhvC ![]() 7zhxC ![]() 7zhyC ![]() 7zhzC C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Protein / Sugars , 2 types, 3 molecules AB![](data/chem/img/BG6.gif)
![](data/chem/img/BG6.gif)
#1: Protein | Mass: 63407.887 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: A2CIL3, glucose-6-phosphate dehydrogenase (NADP+) #5: Sugar | ChemComp-BG6 / | |
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-Non-polymers , 4 types, 12 molecules ![](data/chem/img/NDP.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-SO4 / #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.96 Å3/Da / Density % sol: 58.39 % |
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Crystal grow | Temperature: 283 K / Method: vapor diffusion, sitting drop / Details: 12 % PEG 3000 and 200 mM ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 21, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9999 Å / Relative weight: 1 |
Reflection | Resolution: 3.3→49.3 Å / Num. obs: 22716 / % possible obs: 99.1 % / Redundancy: 5.1 % / Biso Wilson estimate: 124.7 Å2 / CC1/2: 1 / Net I/σ(I): 9.7 |
Reflection shell | Resolution: 3.3→3.4 Å / Mean I/σ(I) obs: 1.3 / Num. unique obs: 11462 / CC1/2: 0.7 / % possible all: 98.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: D_1292122100 Resolution: 3.3→49.3 Å / SU ML: 0.6118 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 36.4726 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 144.88 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.3→49.3 Å
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Refine LS restraints |
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LS refinement shell |
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