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- PDB-4ddm: Pantothenate synthetase in complex with 2,1,3-benzothiadiazole-5-... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4ddm | ||||||
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Title | Pantothenate synthetase in complex with 2,1,3-benzothiadiazole-5-carboxylic acid | ||||||
![]() | Pantothenate synthetase | ||||||
![]() | ligase/ligase inhibitor / Fragment-based drug discovery / Alpha Beta/Adenine nucleotide alpha hydrolase-like / pantoate and b-Ala binding / 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 / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Silvestre, H.L. | ||||||
![]() | ![]() 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 | ![]() | 129.6 KB | Display | ![]() |
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PDB format | ![]() | 101.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4ddhC ![]() 4ddkC ![]() 4de5C ![]() 4ef6C ![]() 4efkC ![]() 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: 31571.178 Da / Num. of mol.: 2 / Mutation: T2A, E77G 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 , 5 types, 497 molecules ![](data/chem/img/GOL.gif)
![](data/chem/img/EOH.gif)
![](data/chem/img/0HO.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/EOH.gif)
![](data/chem/img/0HO.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | ChemComp-EDO / | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.13 Å3/Da / Density % sol: 42.34 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 10-15% PEG 3000, 150 mM Li2SO4, 0.1 M imidazole, 2% ethanol, 10% ethylene glycol, 20 mM MgCl2 , pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 294K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 17, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Resolution: 1.83→40.42 Å / Num. all: 208448 / Num. obs: 48452 / % possible obs: 99.9 % / Redundancy: 4.3 % / Biso Wilson estimate: 22.22 Å2 / Rmerge(I) obs: 0.068 / Rsym value: 0.068 / Net I/σ(I): 17 |
Reflection shell | Resolution: 1.83→1.95 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.531 / Mean I/σ(I) obs: 2.6 / % possible all: 100 |
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Processing
Software | Name: REFMAC / Version: 5.5.0102 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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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: 25.72 Å2
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Refinement step | Cycle: LAST / Resolution: 1.83→35.52 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.83→1.877 Å / Total num. of bins used: 20
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