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- PDB-7edz: Crystal Structure of human PPCS in complex with P-HoPan and AMPPNP -
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Open data
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Basic information
Entry | Database: PDB / ID: 7edz | ||||||
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Title | Crystal Structure of human PPCS in complex with P-HoPan and AMPPNP | ||||||
![]() | Phosphopantothenate--cysteine ligase | ||||||
![]() | LIGASE / Phosphopantothenoylcysteine synthetase | ||||||
Function / homology | ![]() phosphopantothenate-cysteine ligase (ATP) / phosphopantothenate--cysteine ligase activity / Coenzyme A biosynthesis / acetyl-CoA biosynthetic process / heart process / coenzyme A biosynthetic process / protein homodimerization activity / ATP binding / identical protein binding / nucleus ...phosphopantothenate-cysteine ligase (ATP) / phosphopantothenate--cysteine ligase activity / Coenzyme A biosynthesis / acetyl-CoA biosynthetic process / heart process / coenzyme A biosynthetic process / protein homodimerization activity / ATP binding / identical protein binding / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Sharma, N. / Mostert, K.J. / Strauss, E. / Anand, R. | ||||||
Funding support | ![]()
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![]() | ![]() Title: The Coenzyme A Level Modulator Hopantenate (HoPan) Inhibits Phosphopantotenoylcysteine Synthetase Activity. Authors: Mostert, K.J. / Sharma, N. / van der Zwaag, M. / Staats, R. / Koekemoer, L. / Anand, R. / Sibon, O.C.M. / Strauss, 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 | ![]() | 260.3 KB | Display | ![]() |
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PDB format | ![]() | 209 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.8 MB | Display | ![]() |
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Full document | ![]() | 2.8 MB | Display | |
Data in XML | ![]() | 51.8 KB | Display | |
Data in CIF | ![]() | 71.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1p9oS S: Starting model for refinement |
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Similar 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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3 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
-Protein , 1 types, 4 molecules DCBA
#1: Protein | Mass: 34035.062 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q9HAB8, phosphopantothenate-cysteine ligase (ATP) |
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-Non-polymers , 6 types, 479 molecules ![](data/chem/img/ANP.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/J1O.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/J1O.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-ANP / #3: Chemical | ChemComp-SO4 / #4: Chemical | ChemComp-MG / #5: Chemical | ChemComp-J1O / #6: Chemical | ChemComp-GOL / #7: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.7 Å3/Da / Density % sol: 54.4 % |
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Crystal grow | Temperature: 280 K / Method: vapor diffusion, hanging drop Details: 0.2 M Lithium Sulfate Monohydrate, 0.1 M Tris HCl, 30% PEG 4000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 2, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.987 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→36.72 Å / Num. obs: 103396 / % possible obs: 98.2 % / Redundancy: 8.9 % / CC1/2: 0.996 / Net I/σ(I): 10.79 |
Reflection shell | Resolution: 1.95→1.99 Å / Num. unique obs: 7572 / CC1/2: 0.928 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1P9O Resolution: 1.95→36.72 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.955 / SU B: 3.574 / SU ML: 0.098 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.148 / ESU R Free: 0.132 / Stereochemistry target values: MAXIMUM LIKELIHOOD 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 128.02 Å2 / Biso mean: 37.02 Å2 / Biso min: 18.06 Å2
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Refinement step | Cycle: final / Resolution: 1.95→36.72 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.95→2.001 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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