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- PDB-6awi: Staphylococcus aureus Type II pantothenate kinase in complex with... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6awi | ||||||
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Title | Staphylococcus aureus Type II pantothenate kinase in complex with ADP and pantothenate analog Deoxy-N5Pan | ||||||
![]() | Type II pantothenate kinase | ||||||
![]() | TRANSFERASE / Staphylococcus aureus / SaPanK / ADP / pantothenate analog | ||||||
Function / homology | ![]() pantothenate kinase / pantothenate kinase activity / coenzyme A biosynthetic process / ATP binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Chen, Y. / Antoshchenko, T. / Strauss, E. / Barnard, L. / Huang, Y.H. | ||||||
![]() | ![]() Title: Structure-based identification of uncompetitive inhibitors for Staphylococcus aureus pantothenate kinase. Authors: Chen, Y. / Antoshchenko, T. / Strauss, E. / Barnard, L. / Huang, Y.H. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 226.8 KB | Display | ![]() |
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PDB format | ![]() | 182.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related 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: 28997.770 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: coaW, AYM28_11860, AYM37_11860, ERS072738_01917, ERS074020_01878, HMPREF3211_02599 Production host: ![]() ![]() References: UniProt: A0A0D6HHM8, UniProt: Q2FWC7*PLUS, pantothenate kinase #2: Chemical | ChemComp-ADP / #3: Chemical | ChemComp-C0D / ( #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.38 Å3/Da / Density % sol: 48.4 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 30% PEG4000, 0.2 M lithium sulfate, 0.1 M Tris-HCl, pH 8.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 30, 2016 |
Radiation | Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→132.09 Å / Num. obs: 101733 / % possible obs: 99.6 % / Redundancy: 4.46 % / Net I/σ(I): 10.91 |
Reflection shell | Highest resolution: 1.8 Å |
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Processing
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Refinement | Method to determine structure: ![]() Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 92.85 Å2 / Biso mean: 28.973 Å2 / Biso min: 9.5 Å2
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Refinement step | Cycle: final / Resolution: 1.8→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.847 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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