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Open data
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Basic information
Entry | Database: PDB / ID: 6x4k | ||||||
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Title | PANK3 complex structure with compound PZ-2890 | ||||||
![]() | Pantothenate kinase 3 | ||||||
![]() | TRANSFERASE / PANK / Substrate / Complex / Pantothenate kinase | ||||||
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. | ||||||
![]() | ![]() Title: LipE guided discovery of isopropylphenyl pyridazines as pantothenate kinase modulators. Authors: Sharma, L.K. / Yun, M.K. / Subramanian, C. / Tangallapally, R. / Jackowski, S. / Rock, C.O. / White, S.W. / 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 | ![]() | 187.6 KB | Display | ![]() |
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PDB format | ![]() | 121.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 940.9 KB | Display | ![]() |
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Full document | ![]() | 942.7 KB | Display | |
Data in XML | ![]() | 15.8 KB | Display | |
Data in CIF | ![]() | 21.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6x4jC ![]() 6x4lC ![]() 5kprS 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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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 , 6 types, 101 molecules ![](data/chem/img/UOP.gif)
![](data/chem/img/ANP.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/ANP.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-UOP / | ||||
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#3: Chemical | ChemComp-ANP / | ||||
#4: Chemical | ChemComp-MG / | ||||
#5: Chemical | #6: Chemical | ChemComp-CL / | #7: 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: 2.29 Å3/Da / Density % sol: 46.37 % |
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Crystal grow | Temperature: 291.15 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: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 29, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→50 Å / Num. obs: 22980 / % possible obs: 99.9 % / Redundancy: 6.2 % / Biso Wilson estimate: 36.27 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.102 / Net I/σ(I): 21.8 |
Reflection shell | Resolution: 2.1→2.15 Å / Rmerge(I) obs: 0.851 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 1644 / CC1/2: 0.752 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5KPR Resolution: 2.1→36.28 Å / SU ML: 0.2255 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 22.0182 / 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: 44.13 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→36.28 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: -21.9321966524 Å / Origin y: 22.0194567906 Å / Origin z: -6.14782359865 Å
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Refinement TLS group | Selection details: (chain 'A' and resid 11 through 369) |