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- PDB-6sy7: Structure of Trypanosome Brucei Phosphofructokinase in complex wi... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6sy7 | ||||||
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Title | Structure of Trypanosome Brucei Phosphofructokinase in complex with AMP. | ||||||
![]() | ATP-dependent 6-phosphofructokinase | ||||||
![]() | TRANSFERASE / Glycolysis / AMP / Allostery | ||||||
Function / homology | ![]() 6-phosphofructokinase / 6-phosphofructokinase activity / glycosome / fructose 6-phosphate metabolic process / phosphate ion binding / glycolytic process / ATP binding / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | McNae, I.W. / Vasquez-Valdivieso, M.G. / Walkinshaw, M.D. | ||||||
![]() | ![]() Title: Kinetic and structural studies of Trypanosoma and Leishmania phosphofructokinases show evolutionary divergence and identify AMP as a switch regulating glycolysis versus gluconeogenesis. Authors: Fernandes, P.M. / Kinkead, J. / McNae, I.W. / Vasquez-Valdivieso, M. / Wear, M.A. / Michels, P.A.M. / Walkinshaw, M.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 | ![]() | 707.2 KB | Display | ![]() |
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PDB format | ![]() | 576.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.4 MB | Display | ![]() |
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Full document | ![]() | 2.4 MB | Display | |
Data in XML | ![]() | 69.3 KB | Display | |
Data in CIF | ![]() | 107.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3f5mS 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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Unit cell |
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Components
#1: Protein | Mass: 53593.348 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-BNZ / #3: Chemical | ChemComp-GOL / #4: Chemical | ChemComp-AMP / #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.51 Å3/Da / Density % sol: 50.98 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / Details: PEG 8000, sodium cacodylate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 15, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9159 Å / Relative weight: 1 |
Reflection | Resolution: 2.75→39.81 Å / Num. obs: 111370 / % possible obs: 99 % / Redundancy: 3.8 % / CC1/2: 0.997 / Rmerge(I) obs: 0.075 / Rrim(I) all: 0.1 / Rsym value: 0.05 / Net I/σ(I): 9.6 |
Reflection shell | Resolution: 2.75→2.848 Å / Rmerge(I) obs: 0.604 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 5467 / CC1/2: 0.694 / Rpim(I) all: 0.398 / Rrim(I) all: 0.808 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3F5M Resolution: 2.75→39.81 Å / Cross valid method: FREE R-VALUE /
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Displacement parameters | Biso mean: 34.85 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.75→39.81 Å
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Refine LS restraints |
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