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Yorodumi- PDB-5ag7: CRYSTAL STRUCTURE OF LEISHMANIA MAJOR N-MYRISTOYLTRANSFERASE (NMT... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5ag7 | ||||||
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Title | CRYSTAL STRUCTURE OF LEISHMANIA MAJOR N-MYRISTOYLTRANSFERASE (NMT) WITH BOUND MYRISTOYL-COA AND A BENZOMORPHOLINE LIGAND | ||||||
Components | GLYCYLPEPTIDE N-TETRADECANOYLTRANSFERASE | ||||||
Keywords | TRANSFERASE / N-MYRISTOYLTRANSFERASE / NMT / ACYLTRANSFERASE / DRUG DISCOVERY | ||||||
Function / homology | Function and homology information glycylpeptide N-tetradecanoyltransferase / glycylpeptide N-tetradecanoyltransferase activity / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | LEISHMANIA MAJOR (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | 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. | ||||||
Citation | Journal: Chemmedchem / Year: 2015 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ag7.cif.gz | 101.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ag7.ent.gz | 76.1 KB | Display | PDB format |
PDBx/mmJSON format | 5ag7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5ag7_validation.pdf.gz | 680.3 KB | Display | wwPDB validaton report |
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Full document | 5ag7_full_validation.pdf.gz | 689 KB | Display | |
Data in XML | 5ag7_validation.xml.gz | 19.1 KB | Display | |
Data in CIF | 5ag7_validation.cif.gz | 26.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ag/5ag7 ftp://data.pdbj.org/pub/pdb/validation_reports/ag/5ag7 | HTTPS FTP |
-Related structure data
Related structure data | 5ag4C 5ag5C 5ag6C 5ageC 3h5zS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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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.) LEISHMANIA MAJOR (eukaryote) / Production host: ESCHERICHIA COLI (E. coli) References: UniProt: Q4Q5S8, glycylpeptide N-tetradecanoyltransferase |
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#2: Chemical | ChemComp-XXL / |
#3: Chemical | ChemComp-MYA / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.26 Å3/Da / Density % sol: 45.69 % / Description: NONE |
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Crystal grow | pH: 5.5 / Details: 25.9%PEG1500,0.2M NACL, 0.1M CACODYLATE PH 5.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.9334 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Oct 28, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9334 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→20 Å / Num. obs: 13076 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 12 |
Reflection shell | Resolution: 2.6→2.69 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 2 / % possible all: 99.9 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3H5Z Resolution: 2.6→19.88 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.888 / SU B: 12.958 / SU ML: 0.281 / Cross valid method: THROUGHOUT / ESU R Free: 0.384 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 35.924 Å2
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Refinement step | Cycle: LAST / Resolution: 2.6→19.88 Å
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