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- PDB-6tw6: Plasmodium vivax N-myristoyltransferase with bound indazole inhib... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6tw6 | ||||||
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Title | Plasmodium vivax N-myristoyltransferase with bound indazole inhibitor IMP-923 | ||||||
![]() | Glycylpeptide N-tetradecanoyltransferase | ||||||
![]() | TRANSFERASE / myristoylation / malaria / indazole inhibitor | ||||||
Function / homology | ![]() glycylpeptide N-tetradecanoyltransferase / glycylpeptide N-tetradecanoyltransferase activity / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Brannigan, J.A. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Plasmodium vivax N-myristoyltransferase with bound indazole inhibitor IMP-923 Authors: Brannigan, J.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 | ![]() | 305.6 KB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
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
-Protein , 1 types, 3 molecules AAABBBCCC
#1: Protein | Mass: 45369.906 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: A5K1A2, glycylpeptide N-tetradecanoyltransferase |
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-Non-polymers , 7 types, 1632 molecules ![](data/chem/img/NHW.gif)
![](data/chem/img/NZE.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/DMS.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/NZE.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/DMS.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | ChemComp-SO4 / | #6: Chemical | #7: Chemical | ChemComp-DMS / #8: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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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 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 0.2 M AS, 25% PEG 3350, 0.1 M Bis-Tris |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Nov 30, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→50.381 Å / Num. obs: 139024 / % possible obs: 100 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.125 / Net I/σ(I): 9.8 |
Reflection shell | Resolution: 1.7→1.73 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.817 / Mean I/σ(I) obs: 2 / Num. unique obs: 6789 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Details: Hydrogens have been added in their riding positions
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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 mean: 16.734 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→50.381 Å
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Refine LS restraints |
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LS refinement shell |
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