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- PDB-5age: CRYSTAL STRUCTURE OF LEISHMANIA MAJOR N-MYRISTOYLTRANSFERASE (NMT... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5age | ||||||
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Title | CRYSTAL STRUCTURE OF LEISHMANIA MAJOR N-MYRISTOYLTRANSFERASE (NMT) WITH BOUND MYRISTOYL-COA AND A BENZOMORPHOLINONE LIGAND | ||||||
![]() | GLYCYLPEPTIDE N-TETRADECANOYLTRANSFERASE | ||||||
![]() | TRANSFERASE / NMT / ACYLTRANSFERASE / DRUG DISCOVERY | ||||||
Function / homology | ![]() glycylpeptide N-tetradecanoyltransferase / glycylpeptide N-tetradecanoyltransferase activity / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Robinson, D.A. / Spinks, D. / Smith, V.C. / Thompson, S. / Smith, A. / Torrie, L.S. / McElroy, S.P. / Brand, S. / Brenk, R. / Frearson, J.A. ...Robinson, D.A. / Spinks, D. / Smith, V.C. / Thompson, S. / Smith, A. / Torrie, L.S. / McElroy, S.P. / Brand, S. / Brenk, R. / Frearson, J.A. / Read, K.D. / Wyatt, P.G. / Gilbert, I.H. | ||||||
![]() | ![]() Title: Development of Small-Molecule Trypanosoma Brucei N-Myristoyltransferase Inhibitors: Discovery and Optimisation of a Novel Binding Mode. Authors: Spinks, D. / Smith, V. / Thompson, S. / Robinson, D.A. / Luksch, T. / Smith, A. / Torrie, L.S. / Mcelroy, S. / Stojanovski, L. / Norval, S. / Collie, I.T. / Hallyburton, I. / Rao, B. / ...Authors: Spinks, D. / Smith, V. / Thompson, S. / Robinson, D.A. / Luksch, T. / Smith, A. / Torrie, L.S. / Mcelroy, S. / Stojanovski, L. / Norval, S. / Collie, I.T. / Hallyburton, I. / Rao, B. / Brand, S. / Brenk, R. / Frearson, J.A. / Read, K.D. / Wyatt, P.G. / Gilbert, I.H. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 104.7 KB | Display | ![]() |
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PDB format | ![]() | 78 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 902.1 KB | Display | ![]() |
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Full document | ![]() | 912.1 KB | Display | |
Data in XML | ![]() | 20.4 KB | Display | |
Data in CIF | ![]() | 28.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5ag4C ![]() 5ag5C ![]() 5ag6C ![]() 5ag7C ![]() 3h5zS C: citing same article ( S: Starting model for refinement |
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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: 50513.254 Da / Num. of mol.: 1 / Fragment: RESIDUES 5-421 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q4Q5S8, glycylpeptide N-tetradecanoyltransferase |
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#2: Chemical | ChemComp-M9M / |
#3: Chemical | ChemComp-MYA / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.21 Å3/Da / Density % sol: 44.5 % / Description: NONE |
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Crystal grow | pH: 5.5 / Details: 25.9%PEG1500,0.2M NACL, 0.1M CACODYLATE, PH 5.6 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU IMAGE PLATE / Detector: IMAGE PLATE / Date: Mar 4, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→20 Å / Num. obs: 25800 / % possible obs: 92.3 % / Observed criterion σ(I): 0 / Redundancy: 2.1 % / Biso Wilson estimate: 28 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 22 |
Reflection shell | Resolution: 2→2.03 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 2.7 / % possible all: 85.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3H5Z Resolution: 2→19.75 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.938 / SU B: 4.421 / SU ML: 0.125 / Cross valid method: THROUGHOUT / ESU R: 0.219 / ESU R Free: 0.189 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.722 Å2
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Refinement step | Cycle: LAST / Resolution: 2→19.75 Å
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Refine LS restraints |
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