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- PDB-5o4v: P.vivax NMT with aminomethylindazole and quinoline inhibitors bound -
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Open data
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Basic information
Entry | Database: PDB / ID: 5o4v | ||||||
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Title | P.vivax NMT with aminomethylindazole and quinoline inhibitors bound | ||||||
![]() | Glycylpeptide N-tetradecanoyltransferase | ||||||
![]() | TRANSFERASE / INHIBITOR / MYRISTOYL | ||||||
Function / homology | ![]() glycylpeptide N-tetradecanoyltransferase / glycylpeptide N-tetradecanoyltransferase activity / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Brannigan, J.A. / Wilkinson, A.J. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Fragment-derived inhibitors of human N-myristoyltransferase block capsid assembly and replication of the common cold virus. Authors: Mousnier, A. / Bell, A.S. / Swieboda, D.P. / Morales-Sanfrutos, J. / Perez-Dorado, I. / Brannigan, J.A. / Newman, J. / Ritzefeld, M. / Hutton, J.A. / Guedan, A. / Asfor, A.S. / Robinson, S.W. ...Authors: Mousnier, A. / Bell, A.S. / Swieboda, D.P. / Morales-Sanfrutos, J. / Perez-Dorado, I. / Brannigan, J.A. / Newman, J. / Ritzefeld, M. / Hutton, J.A. / Guedan, A. / Asfor, A.S. / Robinson, S.W. / Hopkins-Navratilova, I. / Wilkinson, A.J. / Johnston, S.L. / Leatherbarrow, R.J. / Tuthill, T.J. / Solari, R. / Tate, E.W. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 292.5 KB | Display | ![]() |
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PDB format | ![]() | 233.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.8 MB | Display | ![]() |
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Full document | ![]() | 1.8 MB | Display | |
Data in XML | ![]() | 57.6 KB | Display | |
Data in CIF | ![]() | 86.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5mu6C ![]() 5o48SC ![]() 5o6hC ![]() 5o6jC 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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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 ABC
#1: Protein | Mass: 45059.559 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: PVX_085815 / Production host: ![]() ![]() References: UniProt: A5K1A2, glycylpeptide N-tetradecanoyltransferase |
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-Non-polymers , 8 types, 1192 molecules ![](data/chem/img/NHW.gif)
![](data/chem/img/9K2.gif)
![](data/chem/img/DMS.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/9KZ.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/9K2.gif)
![](data/chem/img/DMS.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/9KZ.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | #6: Chemical | #7: Chemical | ChemComp-SO4 / #8: Chemical | #9: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.36 Å3/Da / Density % sol: 47.84 % |
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Crystal grow | Temperature: 292 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 |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Oct 11, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97949 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→90 Å / Num. obs: 139052 / % possible obs: 99.9 % / Redundancy: 6.2 % / Biso Wilson estimate: 12.8 Å2 / CC1/2: 0.986 / Rmerge(I) obs: 0.171 / Rpim(I) all: 0.111 / Net I/σ(I): 6.4 |
Reflection shell | Resolution: 1.7→1.73 Å / Redundancy: 6.4 % / Rmerge(I) obs: 1.399 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 6801 / CC1/2: 0.36 / Rpim(I) all: 0.9 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5O48 Resolution: 1.7→89.53 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.916 / SU B: 3.768 / SU ML: 0.114 / Cross valid method: THROUGHOUT / ESU R: 0.133 / ESU R Free: 0.133 / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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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: 20.924 Å2
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Refinement step | Cycle: 1 / Resolution: 1.7→89.53 Å
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Refine LS restraints |
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