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- PDB-6avp: 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: 6avp | ||||||
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Title | Staphylococcus aureus Type II pantothenate kinase in complex with ADP and pantothenate analog Phosphate-MeO-N5Pan | ||||||
![]() | Type II pantothenate kinase | ||||||
![]() | TRANSFERASE / Staphylococcus aureus / SaPanK / ADP / pantothenate analog | ||||||
Function / homology | ![]() pantothenate kinase / pantothenate kinase activity / coenzyme A biosynthetic process / phosphorylation / ATP binding / cytoplasm / 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 | ![]() | 218.4 KB | Display | ![]() |
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PDB format | ![]() | 174.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.3 MB | Display | ![]() |
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Full document | ![]() | 2.3 MB | Display | |
Data in XML | ![]() | 41.4 KB | Display | |
Data in CIF | ![]() | 55.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-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: 28868.654 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: coaW, ERS072840_01840, ERS073071_01656, ERS073583_01730, SAMEA2236422_02154, SAMEA2236459_02267, SAMEA2384700_01964, SAMEA2384800_02212, SAMEA2384856_02334, SAMEA2445640_02323 Production host: ![]() ![]() References: UniProt: A0A167Z3Z6, UniProt: Q2FWC7*PLUS, pantothenate kinase #2: Chemical | ChemComp-ADP / #3: Chemical | ChemComp-N7E / #4: Chemical | ChemComp-MG / #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.34 Å3/Da / Density % sol: 47.45 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 25% PEG3350, 0.2 M lithium sulfate, 0.1 M Bis-Tris, pH 6.5 |
-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: 2.3→131.35 Å / Num. obs: 47658 / % possible obs: 99.4 % / Redundancy: 3.49 % / Net I/σ(I): 8.39 |
Reflection shell | Highest resolution: 2.3 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: 115.57 Å2 / Biso mean: 39.87 Å2 / Biso min: 12.44 Å2
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Refinement step | Cycle: final / Resolution: 2.3→131.35 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.36 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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