+Open data
-Basic information
Entry | Database: PDB / ID: 4unr | ||||||
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Title | Mtb TMK in complex with compound 23 | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 1.98 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 | 4unr.cif.gz | 155.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4unr.ent.gz | 123.5 KB | Display | PDB format |
PDBx/mmJSON format | 4unr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/un/4unr ftp://data.pdbj.org/pub/pdb/validation_reports/un/4unr | HTTPS FTP |
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-Related structure data
Related structure data | 4unnC 4unpC 4unqC 4unsC 1g3uS 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 22264.113 Da / Num. of mol.: 2 / Fragment: RESIDUES 1-210 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) Gene: tmk, tmk_1, tmk_2, DKC2_3451, DSI35_30710, ERS007657_00125, ERS007661_00085, ERS007679_02297, ERS007681_01491, ERS007703_02607, ERS007741_01144, ERS023446_00222, ERS024213_00798, ERS027644_ ...Gene: tmk, tmk_1, tmk_2, DKC2_3451, DSI35_30710, ERS007657_00125, ERS007661_00085, ERS007679_02297, ERS007681_01491, ERS007703_02607, ERS007741_01144, ERS023446_00222, ERS024213_00798, ERS027644_01165, ERS027646_01076, ERS027651_00812, ERS027652_02895, ERS027653_00561, ERS027654_03560, ERS027656_02366, ERS027659_02658, ERS027666_03206, ERS031537_04492, ERS124361_01566, EU767_17775, EU768_12605, EU769_05785, EU770_08300, EU771_12795, EU773_12630, EU774_05685, EU775_05915, EU776_12880, EU777_03925, EUB02_06795, EUB03_06915, EUB06_16595, EUB07_02595, EUB08_14260, EUB09_06965, EUB10_01690, EUB11_02810, EUB12_02780, EUB13_09520, EUB14_09750, EUB16_09100, SAMEA2682835_07050, SAMEA2683035_03767 Production host: ESCHERICHIA COLI (E. coli) References: UniProt: A0A045HB39, UniProt: P9WKE1*PLUS, dTMP kinase #2: Chemical | #3: Chemical | #4: 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: 2.64 Å3/Da / Density % sol: 53.42 % / Description: NONE |
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Crystal grow | Method: vapor diffusion, hanging drop / Details: Well soln: 0.1M PCTP, pH6.8, 4.5M NaCl |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E / Wavelength: 1.5418 |
Detector | Type: RIGAKU CCD / Detector: CCD / Date: Mar 31, 2010 / Details: MIRRORS |
Radiation | Monochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.98→71 Å / Num. obs: 31560 / % possible obs: 99.1 % / Observed criterion σ(I): 2 / Redundancy: 5.1 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 12.3 |
Reflection shell | Resolution: 1.98→2.1 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 2.3 / % possible all: 95.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1G3U Resolution: 1.98→65.39 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.94 / SU B: 7.18 / SU ML: 0.094 / Cross valid method: THROUGHOUT / ESU R: 0.15 / ESU R Free: 0.135 / 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: 29.771 Å2
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Refinement step | Cycle: LAST / Resolution: 1.98→65.39 Å
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Refine LS restraints |
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