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- PDB-5t6c: Crystal structure of Aspergillus fumigatus N-myristoyl transferas... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5t6c | |||||||||
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Title | Crystal structure of Aspergillus fumigatus N-myristoyl transferase in complex with myristoyl CoA and a dichloro-methylpyridinyl-methoxy-phenyl-pyridine piperazine ligand | |||||||||
![]() | Glycylpeptide N-tetradecanoyltransferase | |||||||||
![]() | TRANSFERASE / ACYLTRANSFERASE / DRUG DISCOVERY | |||||||||
Function / homology | ![]() glycylpeptide N-tetradecanoyltransferase / glycylpeptide N-tetradecanoyltransferase activity / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Robinson, D.A. / Wyatt, P.G. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Design and Synthesis of Brain Penetrant Trypanocidal N-Myristoyltransferase Inhibitors. Authors: Bayliss, T. / Robinson, D.A. / Smith, V.C. / Brand, S. / McElroy, S.P. / Torrie, L.S. / Mpamhanga, C. / Norval, S. / Stojanovski, L. / Brenk, R. / Frearson, J.A. / Read, K.D. / Gilbert, I.H. / Wyatt, P.G. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 112.3 KB | Display | ![]() |
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PDB format | ![]() | 81.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 973.5 KB | Display | ![]() |
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Full document | ![]() | 989.1 KB | Display | |
Data in XML | ![]() | 24.9 KB | Display | |
Data in CIF | ![]() | 37 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5t5uC ![]() 5t6eC ![]() 5t6hC ![]() 4caxS 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: 47443.250 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: ATCC MYA-4609 / Af293 / CBS 101355 / FGSC A1100 / Gene: nmt1, AFUA_4G08070 / Plasmid: PGEX-6P1 / Production host: ![]() ![]() References: UniProt: Q9UVX3, glycylpeptide N-tetradecanoyltransferase |
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#2: Chemical | ChemComp-MYA / |
#3: Chemical | ChemComp-75S / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.52 Å3/Da / Density % sol: 51.24 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / Details: 25%PEG3350,0.2M NACL |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 11, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→38.5 Å / Num. obs: 36493 / % possible obs: 99 % / Redundancy: 4.4 % / Biso Wilson estimate: 9.2 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.084 / Net I/σ(I): 13.8 |
Reflection shell | Resolution: 1.9→1.94 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.335 / Mean I/σ(I) obs: 4.3 / CC1/2: 0.94 / % possible all: 99.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4CAX Resolution: 1.9→38 Å / Cor.coef. Fo:Fc: 0.908 / Cor.coef. Fo:Fc free: 0.881 / SU B: 4.111 / SU ML: 0.115 / Cross valid method: THROUGHOUT / ESU R: 0.193 / ESU R Free: 0.166 / Details: HYDROGENS HAVE BEEN ADDED IN THE 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: 16.483 Å2
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Refinement step | Cycle: 1 / Resolution: 1.9→38 Å
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Refine LS restraints |
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