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- PDB-4b11: Plasmodium vivax N-myristoyltransferase with a bound benzofuran i... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4b11 | ||||||
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Title | Plasmodium vivax N-myristoyltransferase with a bound benzofuran inhibitor (compound 13) | ||||||
![]() | GLYCYLPEPTIDE N-TETRADECANOYLTRANSFERASE | ||||||
![]() | TRANSFERASE / MYRISTOYLTRANSFERASE / MALARIA / DRUG DESIGN | ||||||
Function / homology | ![]() glycylpeptide N-tetradecanoyltransferase / glycylpeptide N-tetradecanoyltransferase activity / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Yu, Z. / Brannigan, J.A. / Moss, D.K. / Brzozowski, A.M. / Wilkinson, A.J. / Holder, A.A. / Tate, E.W. / Leatherbarrow, R.J. | ||||||
![]() | ![]() Title: Design and Synthesis of Inhibitors of Plasmodium Falciparum N-Myristoyltransferase, a Promising Target for Anti-Malarial Drug Discovery. Authors: Yu, Z. / Brannigan, J.A. / Moss, D.K. / Brzozowski, A.M. / Wilkinson, A.J. / Holder, A.A. / Tate, E.W. / Leatherbarrow, R.J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 292.8 KB | Display | ![]() |
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PDB format | ![]() | 236.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.9 MB | Display | ![]() |
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Full document | ![]() | 2 MB | Display | |
Data in XML | ![]() | 61.4 KB | Display | |
Data in CIF | ![]() | 92.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4b10SC ![]() 4b12C ![]() 4b13C ![]() 4b14C S: Starting model for refinement 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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3 | ![]()
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Unit cell |
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Components
-Protein , 1 types, 3 molecules ABC
#1: Protein | Mass: 45077.594 Da / Num. of mol.: 3 / Fragment: RESIDUES 27-410 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Description: SYNTHETIC GENE / Plasmid: PET28 DERIVATIVE / Production host: ![]() ![]() References: UniProt: A5K1A2, glycylpeptide N-tetradecanoyltransferase |
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-Non-polymers , 7 types, 1434 molecules ![](data/chem/img/7I1.gif)
![](data/chem/img/NHW.gif)
![](data/chem/img/DMS.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/NHW.gif)
![](data/chem/img/DMS.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | ChemComp-SO4 / | #6: Chemical | ChemComp-CL / #7: Chemical | #8: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.22 Å3/Da / Density % sol: 44.5 % / Description: NONE |
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Crystal grow | pH: 6 Details: 0.2 M AMMONIUM SULPHATE, 24-26 % PEG 3350, 0.1 M BIS TRIS PH 6.0 - 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 23, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.59→71 Å / Num. obs: 161262 / % possible obs: 99.7 % / Observed criterion σ(I): 2 / Redundancy: 7.2 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 12.2 |
Reflection shell | Resolution: 1.59→1.63 Å / Redundancy: 7 % / Rmerge(I) obs: 0.66 / Mean I/σ(I) obs: 2.9 / % possible all: 99.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 4B10 Resolution: 1.59→70.72 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.937 / SU B: 1.837 / SU ML: 0.065 / Cross valid method: THROUGHOUT / ESU R: 0.091 / ESU R Free: 0.097 / 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 mean: 16.608 Å2
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Refinement step | Cycle: LAST / Resolution: 1.59→70.72 Å
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Refine LS restraints |
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