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Yorodumi- PDB-6c67: Mycobacterium tuberculosis adenosine kinase bound to iodotubercidin -
+Open data
-Basic information
Entry | Database: PDB / ID: 6c67 | ||||||||||||
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Title | Mycobacterium tuberculosis adenosine kinase bound to iodotubercidin | ||||||||||||
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 / dGTP binding / AMP salvage / purine ribonucleoside salvage / phosphorylation / GTP binding / magnesium ion binding / ATP binding / plasma membrane Similarity search - Function | ||||||||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.11 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 | 6c67.cif.gz | 235.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6c67.ent.gz | 190.4 KB | Display | PDB format |
PDBx/mmJSON format | 6c67.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c6/6c67 ftp://data.pdbj.org/pub/pdb/validation_reports/c6/6c67 | HTTPS FTP |
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-Related structure data
Related structure data | 6c9nC 6c9pC 6c9qC 6c9rC 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
-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.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria) Strain: ATCC 25618 / H37Rv / Gene: adoK, cbhK, Rv2202c, MTCY190.13c / Production host: Escherichia coli (E. coli) / References: UniProt: P9WID5, adenosine kinase |
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-Non-polymers , 5 types, 268 molecules
#2: Chemical | ChemComp-5ID / ( #3: Chemical | #4: Chemical | ChemComp-GOL / | #5: Chemical | #6: 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: 2.29 Å3/Da / Density % sol: 46.25 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop Details: 0.1 M HEPES, pH 7.5, 2.0 M ammonium sulfate, 2.0% PEG400 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 25, 2013 |
Radiation | Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.105→34.69 Å / Num. obs: 34540 / % possible obs: 96.5 % / Redundancy: 7.3 % / Biso Wilson estimate: 40.73 Å2 / Rmerge(I) obs: 0.0793 / Net I/σ(I): 23.36 |
Reflection shell | Resolution: 2.11→2.18 Å / Rmerge(I) obs: 0.2468 / Num. unique obs: 3485 / CC1/2: 0.985 / Rpim(I) all: 0.09564 / Rrim(I) all: 0.2648 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 2PKM Resolution: 2.11→34.69 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 26.01 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.11→34.69 Å
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Refine LS restraints |
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LS refinement shell |
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