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- PDB-6qde: Leishmania major N-myristoyltransferase in complex with thienopyr... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6qde | ||||||
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Title | Leishmania major N-myristoyltransferase in complex with thienopyrimidine inhibitor IMP-0000877 | ||||||
![]() | Glycylpeptide N-tetradecanoyltransferase | ||||||
![]() | TRANSFERASE / myristoylation / benzothiophene / Leishmania | ||||||
Function / homology | ![]() glycylpeptide N-tetradecanoyltransferase / glycylpeptide N-tetradecanoyltransferase activity / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Brannigan, J.A. | ||||||
![]() | ![]() Title: Novel Thienopyrimidine Inhibitors of Leishmania N -Myristoyltransferase with On-Target Activity in Intracellular Amastigotes. Authors: Bell, A.S. / Yu, Z. / Hutton, J.A. / Wright, M.H. / Brannigan, J.A. / Paape, D. / Roberts, S.M. / Sutherell, C.L. / Ritzefeld, M. / Wilkinson, A.J. / Smith, D.F. / Leatherbarrow, R.J. / 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 | ![]() | 121.7 KB | Display | ![]() |
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PDB format | ![]() | 90.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6qd9C ![]() 6qdaC ![]() 6qdbC ![]() 6qdcC ![]() 6qddC ![]() 6qdfC ![]() 6qdgC ![]() 6qdhC ![]() 4cgpS 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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Unit cell |
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Components
#1: Protein | Mass: 48571.242 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q4Q5S8, glycylpeptide N-tetradecanoyltransferase | ||||
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#2: Chemical | ChemComp-MG / | ||||
#3: Chemical | #4: Chemical | ChemComp-MYA / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.23 Å3/Da / Density % sol: 45 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 30% PEG 1500, 0.2 M NACL, 0.1 M NA CACODYLATE, PH 5.5 |
-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: May 28, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92 Å / Relative weight: 1 |
Reflection | Resolution: 1.45→45 Å / Num. obs: 73481 / % possible obs: 98.6 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 8.6 |
Reflection shell | Resolution: 1.45→1.48 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.657 / Mean I/σ(I) obs: 1.7 / % possible all: 98.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4CGP Resolution: 1.45→45 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.949 / SU B: 1.343 / SU ML: 0.05 / Cross valid method: THROUGHOUT / ESU R: 0.068 / ESU R Free: 0.072 / 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: 14.033 Å2
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Refinement step | Cycle: 1 / Resolution: 1.45→45 Å
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Refine LS restraints |
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