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- PDB-6c9v: Mycobacterium tuberculosis adenosine kinase bound to (2R,3S,4R,5R... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6c9v | ||||||||||||
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Title | Mycobacterium tuberculosis adenosine kinase bound to (2R,3S,4R,5R)-2-(hydroxymethyl)-5-(6-(4-phenylpiperazin-1-yl)-9H-purin-9-yl)tetrahydrofuran-3,4-diol | ||||||||||||
![]() | Adenosine kinase | ||||||||||||
![]() | 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 | ![]() adenosine kinase / adenosine kinase activity / ketohexokinase activity / dGTP binding / regulation of glycogen metabolic process / response to sucrose / response to fructose / AMP salvage / fructose metabolic process / purine ribonucleoside salvage ...adenosine kinase / adenosine kinase activity / ketohexokinase activity / dGTP binding / regulation of glycogen metabolic process / 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 Similarity search - Function | ||||||||||||
Biological species | ![]() ![]() | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Crespo, R.A. / TB Structural Genomics Consortium (TBSGC) | ||||||||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 242.3 KB | Display | ![]() |
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PDB format | ![]() | 195.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1016 KB | Display | ![]() |
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Full document | ![]() | 1016.8 KB | Display | |
Data in XML | ![]() | 28.8 KB | Display | |
Data in CIF | ![]() | 44 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6c67C ![]() 6c9nC ![]() 6c9pC ![]() 6c9qC ![]() 6c9rC ![]() 6c9sC ![]() 2pkmS 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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Unit cell |
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 34503.953 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: A5U4N0, UniProt: P9WID5*PLUS, adenosine kinase |
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-Non-polymers , 5 types, 576 molecules ![](data/chem/img/ERS.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/SO4.gif)
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![](data/chem/img/GOL.gif)
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#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | ChemComp-GOL / | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.41 Å3/Da / Density % sol: 48.88 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop Details: 100 mM HEPES, pH 7.5, 2 M ammonium sulfate, 2% PEG400 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
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: 1.701→43.56 Å / Num. obs: 70903 / % possible obs: 99.9 % / Redundancy: 5.1 % / Rmerge(I) obs: 0.09756 / Net I/σ(I): 11.01 |
Reflection shell | Resolution: 1.7→1.76 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.5145 / Mean I/σ(I) obs: 2.22 / % possible all: 98.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2PKM Resolution: 1.7→43.56 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 20.32
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→43.56 Å
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Refine LS restraints |
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LS refinement shell |
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