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- PDB-6gnv: Crystal Structure of Leishmania major N-Myristoyltransferase (NMT... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6gnv | ||||||||||||
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Title | Crystal Structure of Leishmania major N-Myristoyltransferase (NMT) With Bound Myristoyl-CoA and a isopropyl methyl indole aryl sulphonamide ligand | ||||||||||||
![]() | Glycylpeptide N-tetradecanoyltransferase | ||||||||||||
![]() | TRANSFERASE / 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. / Harrison, J.R. / Brand, S. / Smith, V.C. / Thompson, S. / Smith, A. / Davies, K. / Mok, N.Y. / Torrie, L.S. / Collie, I. ...Robinson, D.A. / Harrison, J.R. / Brand, S. / Smith, V.C. / Thompson, S. / Smith, A. / Davies, K. / Mok, N.Y. / Torrie, L.S. / Collie, I. / Hallyburton, I. / Norval, S. / Simeons, F.R.C. / Stojanovski, L. / Frearson, J.A. / Brenk, R. / Wyatt, P.G. / Gilbert, I.H. / Read, K.D. | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: A Molecular Hybridization Approach for the Design of Potent, Highly Selective, and Brain-Penetrant N-Myristoyltransferase Inhibitors. Authors: Harrison, J.R. / Brand, S. / Smith, V. / Robinson, D.A. / Thompson, S. / Smith, A. / Davies, K. / Mok, N. / Torrie, L.S. / Collie, I. / Hallyburton, I. / Norval, S. / Simeons, F.R.C. / ...Authors: Harrison, J.R. / Brand, S. / Smith, V. / Robinson, D.A. / Thompson, S. / Smith, A. / Davies, K. / Mok, N. / Torrie, L.S. / Collie, I. / Hallyburton, I. / Norval, S. / Simeons, F.R.C. / Stojanovski, L. / Frearson, J.A. / Brenk, R. / Wyatt, P.G. / Gilbert, I.H. / Read, K.D. | ||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 108.5 KB | Display | ![]() |
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PDB format | ![]() | 79.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 902 KB | Display | ![]() |
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Full document | ![]() | 914.3 KB | Display | |
Data in XML | ![]() | 21.5 KB | Display | |
Data in CIF | ![]() | 30.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6gnhC ![]() 6gnsC ![]() 6gntC ![]() 6gnuC ![]() 3h5zS 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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Unit cell |
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Components
#1: Protein | Mass: 47263.852 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-MYA / |
#3: Chemical | ChemComp-F5E / ~{ |
#4: Chemical | ChemComp-GOL / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.27 Å3/Da / Density % sol: 45.8 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.6 / Details: 26% PEG1500, 0.2M NACL, 0.1M NACACODYLATE, PH 5.6 / PH range: 4.0-6.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 20, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→48.7 Å / Num. obs: 21349 / % possible obs: 99.4 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.091 / Net I/σ(I): 10.4 |
Reflection shell | Resolution: 2.2→2.32 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.394 / Mean I/σ(I) obs: 3.4 / % possible all: 99.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3h5z Resolution: 2.2→45.21 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.926 / SU B: 5.583 / SU ML: 0.141 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.291 / ESU R Free: 0.202 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 118.47 Å2 / Biso mean: 30.693 Å2 / Biso min: 12.58 Å2
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Refinement step | Cycle: final / Resolution: 2.2→45.21 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.257 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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