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Open data
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Basic information
Entry | Database: PDB / ID: 9d2o | ||||||
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Title | PANK3 complex structure with compound PZ-5351 | ||||||
![]() | 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 | ![]() ![]() ![]() | ||||||
![]() | Yun, M. / Lee, R.E. | ||||||
Funding support | 1items
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![]() | ![]() Title: 2-(4-aminophenyl)acetamide derivatives as Pantothenate Kinase Inhibitors. Authors: Yun, M. / 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 | ![]() | 192.6 KB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 981 KB | Display | ![]() |
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Full document | ![]() | 984.4 KB | Display | |
Data in XML | ![]() | 18.7 KB | Display | |
Data in CIF | ![]() | 25.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 9d2pC 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 , 6 types, 139 molecules 








#2: Chemical | ChemComp-A1A1N / Mass: 441.907 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H21ClFN5O3S / Feature type: SUBJECT OF INVESTIGATION | ||
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#3: Chemical | ChemComp-ACY / | ||
#4: Chemical | ChemComp-ANP / | ||
#5: Chemical | ChemComp-MG / | ||
#6: Chemical | #7: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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Has protein modification | N |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.26 Å3/Da / Density % sol: 45.52 % |
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Crystal grow | Temperature: 293 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 9M / Detector: PIXEL / Date: Jan 31, 2024 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9201 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→34.63 Å / Num. obs: 35586 / % possible obs: 100 % / Redundancy: 12.1 % / Biso Wilson estimate: 27.23 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.088 / Net I/σ(I): 16.5 |
Reflection shell | Resolution: 1.8→1.84 Å / Rmerge(I) obs: 1.287 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 2072 / CC1/2: 0.756 |
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Processing
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Refinement | Method to determine structure: ![]()
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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: 36.17 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→32.04 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: -29.9156674467 Å / Origin y: -7.78950555072 Å / Origin z: 4.95647140828 Å
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Refinement TLS group | Selection details: all |