+Open data
-Basic information
Entry | Database: PDB / ID: 4unn | ||||||
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Title | Mtb TMK in complex with compound 8 | ||||||
Components | THYMIDYLATE KINASE | ||||||
Keywords | TRANSFERASE / ATP TMP PHOSPHOTRANSFERASE | ||||||
Function / homology | Function and homology information TMP metabolic process / dUDP biosynthetic process / dTMP kinase / thymidylate kinase activity / dTDP biosynthetic process / dTTP biosynthetic process / phosphorylation / GTP binding / magnesium ion binding / protein homodimerization activity ...TMP metabolic process / dUDP biosynthetic process / dTMP kinase / thymidylate kinase activity / dTDP biosynthetic process / dTTP biosynthetic process / phosphorylation / GTP binding / magnesium ion binding / protein homodimerization activity / ATP binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | MYCOBACTERIUM TUBERCULOSIS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Read, J.A. / Hussein, S. / Gingell, H. / Tucker, J. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2015 Title: Structure Guided Lead Generation for M. Tuberculosis Thymidylate Kinase (Mtb Tmk): Discovery of 3-Cyanopyridone and 1,6-Naphthyridin-2-One as Potent Inhibitors. Authors: Naik, M. / Raichurkar, A. / Bandodkar, B.S. / Varun, B.V. / Bhat, S. / Kalkhambkar, R. / Murugan, K. / Menon, R. / Bhat, J. / Paul, B. / Iyer, H. / Hussein, S. / Tucker, J.A. / Vogtherr, M. ...Authors: Naik, M. / Raichurkar, A. / Bandodkar, B.S. / Varun, B.V. / Bhat, S. / Kalkhambkar, R. / Murugan, K. / Menon, R. / Bhat, J. / Paul, B. / Iyer, H. / Hussein, S. / Tucker, J.A. / Vogtherr, M. / Embrey, K.J. / Mcmiken, H. / Prasad, S. / Gill, A. / Ugarkar, B.G. / Venkatraman, J. / Read, J. / Panda, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4unn.cif.gz | 146.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4unn.ent.gz | 116.5 KB | Display | PDB format |
PDBx/mmJSON format | 4unn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/un/4unn ftp://data.pdbj.org/pub/pdb/validation_reports/un/4unn | HTTPS FTP |
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-Related structure data
Related structure data | 4unpC 4unqC 4unrC 4unsC 1g3uS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 22630.461 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) MYCOBACTERIUM TUBERCULOSIS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) References: UniProt: F2GKC3, UniProt: P9WKE1*PLUS, dTMP kinase #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.59 Å3/Da / Density % sol: 52.6 % / Description: NONE |
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-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.98 | |||||||||||||||
Detector | Type: ADSC CCD / Detector: CCD / Date: Jan 28, 2009 | |||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 | |||||||||||||||
Reflection twin |
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Reflection | Resolution: 2.5→32.8 Å / Num. obs: 15736 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 3.7 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 7.6 | |||||||||||||||
Reflection shell | Resolution: 2.5→2.64 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 2.6 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1G3U Resolution: 2.5→32.75 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.931 / SU B: 12.85 / SU ML: 0.125 / Cross valid method: THROUGHOUT / ESU R: 0.064 / ESU R Free: 0.043 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.928 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→32.75 Å
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Refine LS restraints |
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