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Open data
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Basic information
Entry | Database: PDB / ID: 7uep | ||||||
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Title | PANK3 complex structure with compound PZ-3860 | ||||||
![]() | Pantothenate kinase 3 | ||||||
![]() | TRANSFERASE / PANK / Substrate / Complex / Pantothenate kinase / Inhibitor / Activator | ||||||
Function / homology | ![]() Coenzyme A biosynthesis / vitamin binding / acetyl-CoA binding / pantothenate kinase / pantothenate kinase activity / coenzyme A biosynthetic process / phosphorylation / protein homodimerization activity / ATP binding / nucleus / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | White, S.W. / Yun, M. / Lee, R.E. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Discovery of hPANK Activators with Improved Pharmacological Properties Authors: Tangallapally, R. / Edwards, A. / Subramanian, C. / Sharma, L.K. / Yun, M. / White, S.W. / Jackowski, S. / Rock, C.O. / Lee, 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 | ![]() | 187.8 KB | Display | ![]() |
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PDB format | ![]() | 121.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 976.5 KB | Display | ![]() |
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Full document | ![]() | 977.8 KB | Display | |
Data in XML | ![]() | 15.6 KB | Display | |
Data in CIF | ![]() | 21.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7ue3C ![]() 7ue4C ![]() 7ue5C ![]() 7ue6C ![]() 7ue7C ![]() 7ueoC ![]() 7ueqC ![]() 7uerC ![]() 7uesC ![]() 7uetC ![]() 7ueuC ![]() 7uevC ![]() 7uexC ![]() 7ueyC ![]() 6b3vS S: Starting model for refinement 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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1 | ![]()
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Unit cell |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 42125.750 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 5 types, 86 molecules ![](data/chem/img/ANP.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/Y93.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/Y93.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-ANP / |
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#3: Chemical | ChemComp-MG / |
#4: Chemical | ChemComp-EDO / |
#5: Chemical | ChemComp-Y93 / |
#6: Water | ChemComp-HOH / |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.31 Å3/Da / Density % sol: 46.73 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.6 / Details: PEG 4000, ammonium acetate, citrate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 18, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. obs: 26853 / % possible obs: 99.6 % / Redundancy: 6.2 % / Biso Wilson estimate: 37.77 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.08 / Net I/σ(I): 26.5 |
Reflection shell | Resolution: 2→2.04 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.805 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 1653 / CC1/2: 0.791 / % possible all: 99.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6B3V Resolution: 2→36.37 Å / SU ML: 0.1992 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 21.0532 / Stereochemistry target values: 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: 47.1 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→36.37 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -22.1104404213 Å / Origin y: 21.8823440195 Å / Origin z: -6.06959412668 Å
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Refinement TLS group | Selection details: (chain 'A' and resid 11 through 369) |