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Open data
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Basic information
Entry | Database: PDB / ID: 5tdf | ||||||
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Title | TEV Cleaved Human ATP Citrate Lyase Bound to 4S hydroxycitrate | ||||||
![]() | (ATP-citrate synthase) x 2 | ||||||
![]() | TRANSFERASE / TEV cleaved / ATP-grasp fold / 4S Hydroxycitrate | ||||||
Function / homology | ![]() ATP citrate synthase activity / ATP citrate synthase / Fatty acyl-CoA biosynthesis / citrate metabolic process / ChREBP activates metabolic gene expression / acetyl-CoA biosynthetic process / oxaloacetate metabolic process / coenzyme A metabolic process / lipid biosynthetic process / cholesterol biosynthetic process ...ATP citrate synthase activity / ATP citrate synthase / Fatty acyl-CoA biosynthesis / citrate metabolic process / ChREBP activates metabolic gene expression / acetyl-CoA biosynthetic process / oxaloacetate metabolic process / coenzyme A metabolic process / lipid biosynthetic process / cholesterol biosynthetic process / tricarboxylic acid cycle / fatty acid biosynthetic process / azurophil granule lumen / ficolin-1-rich granule lumen / Neutrophil degranulation / extracellular exosome / extracellular region / nucleoplasm / ATP binding / membrane / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Hu, J. / Fraser, M.E. | ||||||
![]() | ![]() Title: Binding of hydroxycitrate to human ATP-citrate lyase. Authors: Hu, J. / Komakula, A. / Fraser, M.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 | ![]() | 305.1 KB | Display | ![]() |
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PDB format | ![]() | 255.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 814.2 KB | Display | ![]() |
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Full document | ![]() | 815.5 KB | Display | |
Data in XML | ![]() | 36.4 KB | Display | |
Data in CIF | ![]() | 56.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5tdeC ![]() 5tdmC ![]() 5tdzC ![]() 5te1C ![]() 5teqC ![]() 5tesC ![]() 5tetC 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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Unit cell |
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Components
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 47836.633 Da / Num. of mol.: 1 / Fragment: unp residues 1-425 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Protein | Mass: 35421.570 Da / Num. of mol.: 1 / Fragment: unp residues 488-810 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
-Non-polymers , 6 types, 832 molecules ![](data/chem/img/7A3.gif)
![](data/chem/img/ADP.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/ADE.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/ADP.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/ADE.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-7A3 / | ||||||
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#4: Chemical | ChemComp-ADP / | ||||||
#5: Chemical | #6: Chemical | ChemComp-GOL / #7: Chemical | ChemComp-ADE / | #8: Water | ChemComp-HOH / | |
-Details
Sequence details | THE AMINO-TERMINAL PORTION OF HUMAN ACLY WAS REDESIGNED TO HAVE TEV PROTEASE CLEAVAGE SITES ...THE AMINO-TERMINAL PORTION OF HUMAN ACLY WAS REDESIGNED |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.71 Å3/Da / Density % sol: 54.68 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 8.4 Details: 15% P3350, 100 mM TrisHCl pH 8.4, 150 mM ammonium chloride |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 17, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→41.94 Å / Num. obs: 84385 / % possible obs: 99.6 % / Redundancy: 3.5 % / Net I/σ(I): 8.4 |
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Processing
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Refinement | Resolution: 1.8→41.94 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.15
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→41.94 Å
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Refine LS restraints |
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LS refinement shell |
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