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- PDB-4efk: Pantothenate synthetase in complex with N,N-DIMETHYLTHIOPHENE-3-S... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4efk | ||||||
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Title | Pantothenate synthetase in complex with N,N-DIMETHYLTHIOPHENE-3-SULFONAMIDE | ||||||
![]() | Pantothenate synthetase | ||||||
![]() | ligase/ligase inhibitor / Alpha Beta/3-Layer Sandwich/Rossmann fold / ligase-ligase inhibitor complex | ||||||
Function / homology | ![]() beta-alanine metabolic process / pantoate-beta-alanine ligase (AMP-forming) / pantoate-beta-alanine ligase activity / pantothenate biosynthetic process / manganese ion binding / magnesium ion binding / ATP binding / metal ion binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Ciulli, A. / Silvestre, H.L. / Blundell, T.L. / Abell, C. | ||||||
![]() | ![]() Title: Integrated biophysical approach to fragment screening and validation for fragment-based lead discovery. Authors: Silvestre, H.L. / Blundell, T.L. / Abell, C. / Ciulli, A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 127.6 KB | Display | ![]() |
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PDB format | ![]() | 99.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 503.8 KB | Display | ![]() |
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Full document | ![]() | 520.6 KB | Display | |
Data in XML | ![]() | 29.1 KB | Display | |
Data in CIF | ![]() | 41.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4ddhC ![]() 4ddkC ![]() 4ddmC ![]() 4de5C ![]() 4ef6C ![]() 4fzjC ![]() 4g5fC ![]() 4g5yC 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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2 | ![]()
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Unit cell |
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 31500.100 Da / Num. of mol.: 2 / Fragment: unp residues 1-300 / Mutation: T2A, G77E Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P0A5R0, UniProt: P9WIL5*PLUS, pantoate-beta-alanine ligase (AMP-forming) |
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-Non-polymers , 6 types, 406 molecules ![](data/chem/img/0OC.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/EOH.gif)
![](data/chem/img/IMD.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/EOH.gif)
![](data/chem/img/IMD.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-EOH / #5: Chemical | ChemComp-IMD / | #6: Chemical | ChemComp-SO4 / | #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.23 Å3/Da / Density % sol: 44.75 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 12-14% PEG 3000, 150 mM Li2SO4, 100 mM Imidazole, 2% Ethanol, 5% Glycerol 20 mM MgCl2, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction source | Source: ![]() ![]() ![]() |
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Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: May 16, 2008 / Details: Diamond (001) |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→30 Å / Num. obs: 60243 / % possible obs: 91 % |
Reflection shell | Resolution: 1.7→1.74 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.428 / Mean I/σ(I) obs: 2.1 / % possible all: 91 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.648 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→28.61 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.744 Å / Total num. of bins used: 20
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