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Yorodumi- PDB-6c9r: Mycobacterium tuberculosis adenosine kinase bound to (2R,3S,4R,5R... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6c9r | ||||||||||||
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Title | Mycobacterium tuberculosis adenosine kinase bound to (2R,3S,4R,5R)-2-(hydroxymethyl)-5-(6-(thiophen-3-yl)-9H-purin-9-yl)tetrahydrofuran-3,4-diol | ||||||||||||
Components | Adenosine kinase | ||||||||||||
Keywords | TRANSFERASE/TRANSFERASE INHIBITOR / Nucleoside analog / Complex / Inhibitor / Structural Genomics / PSI-2 / Protein Structure Initiative / TB Structural Genomics Consortium / TBSGC / TRANSFERASE-TRANSFERASE INHIBITOR complex | ||||||||||||
Function / homology | Function and homology information adenosine kinase / adenosine kinase activity / ketohexokinase activity / regulation of glycogen metabolic process / dGTP binding / response to sucrose / response to fructose / AMP salvage / fructose metabolic process / purine ribonucleoside salvage ...adenosine kinase / adenosine kinase activity / ketohexokinase activity / regulation of glycogen metabolic process / dGTP binding / response to sucrose / response to fructose / AMP salvage / fructose metabolic process / purine ribonucleoside salvage / response to zinc ion / response to glucose / response to insulin / GTP binding / magnesium ion binding / ATP binding / plasma membrane / cytoplasm Similarity search - Function | ||||||||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||||||||
Authors | Crespo, R.A. / TB Structural Genomics Consortium (TBSGC) | ||||||||||||
Funding support | United States, 3items
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Citation | Journal: J.Med.Chem. / Year: 2019 Title: Structure-Guided Drug Design of 6-Substituted Adenosine Analogues as Potent Inhibitors of Mycobacterium tuberculosis Adenosine Kinase. Authors: Crespo, R.A. / Dang, Q. / Zhou, N.E. / Guthrie, L.M. / Snavely, T.C. / Dong, W. / Loesch, K.A. / Suzuki, T. / You, L. / Wang, W. / O'Malley, T. / Parish, T. / Olsen, D.B. / Sacchettini, J.C. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6c9r.cif.gz | 253 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6c9r.ent.gz | 204.2 KB | Display | PDB format |
PDBx/mmJSON format | 6c9r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6c9r_validation.pdf.gz | 1.8 MB | Display | wwPDB validaton report |
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Full document | 6c9r_full_validation.pdf.gz | 1.8 MB | Display | |
Data in XML | 6c9r_validation.xml.gz | 27.5 KB | Display | |
Data in CIF | 6c9r_validation.cif.gz | 39.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c9/6c9r ftp://data.pdbj.org/pub/pdb/validation_reports/c9/6c9r | HTTPS FTP |
-Related structure data
Related structure data | 6c67C 6c9nC 6c9pC 6c9qC 6c9sC 6c9vC 2pkmS 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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Unit cell |
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-Components
#1: Protein | Mass: 35980.516 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: adoK, cbhK, MRA_2218 / Production host: Escherichia coli (E. coli) References: UniProt: A5U4N0, UniProt: P9WID5*PLUS, adenosine kinase #2: Chemical | ChemComp-ERJ / #3: Chemical | #4: Chemical | ChemComp-GOL / | #5: 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: 3.48 Å3/Da / Density % sol: 64.64 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / Details: 5.0 M sodium formate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 25, 2017 |
Radiation | Monochromator: double crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 |
Reflection | Resolution: 2.102→44.38 Å / Num. obs: 57583 / % possible obs: 99.7 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.05875 / Net I/σ(I): 11.89 |
Reflection shell | Resolution: 2.1→2.18 Å / Rmerge(I) obs: 0.3148 / Mean I/σ(I) obs: 3.43 / % possible all: 97.9 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2PKM Resolution: 2.1→44.38 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 20.62
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→44.38 Å
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Refine LS restraints |
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LS refinement shell |
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