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Yorodumi- PDB-3q92: X-ray Structure of ketohexokinase in complex with a pyrimidopyrim... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3q92 | ||||||
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Title | X-ray Structure of ketohexokinase in complex with a pyrimidopyrimidine analog 1 | ||||||
Components | Ketohexokinase | ||||||
Keywords | TRANSFERASE/TRANSFERASE INHIBITOR / ketohexokinase / ATP Binding / TRANSFERASE-TRANSFERASE INHIBITOR complex | ||||||
Function / homology | Function and homology information Essential fructosuria / ketohexokinase / ketohexokinase activity / Fructose catabolism / regulation of glycogen metabolic process / response to sucrose / response to fructose / fructose metabolic process / response to zinc ion / response to glucose ...Essential fructosuria / ketohexokinase / ketohexokinase activity / Fructose catabolism / regulation of glycogen metabolic process / response to sucrose / response to fructose / fructose metabolic process / response to zinc ion / response to glucose / response to insulin / extracellular exosome / ATP binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Abad, M.C. | ||||||
Citation | Journal: ACS Med Chem Lett / Year: 2011 Title: Inhibitors of Ketohexokinase: Discovery of Pyrimidinopyrimidines with Specific Substitution that Complements the ATP-Binding Site. Authors: Maryanoff, B.E. / O'Neill, J.C. / McComsey, D.F. / Yabut, S.C. / Luci, D.K. / Jordan, A.D. / Masucci, J.A. / Jones, W.J. / Abad, M.C. / Gibbs, A.C. / Petrounia, I. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3q92.cif.gz | 128.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3q92.ent.gz | 99.4 KB | Display | PDB format |
PDBx/mmJSON format | 3q92.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q9/3q92 ftp://data.pdbj.org/pub/pdb/validation_reports/q9/3q92 | HTTPS FTP |
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-Related structure data
Related structure data | 3qa2C 3qaiC 3nbvS 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: 34076.586 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: KHK / Plasmid: pET28s / Production host: Escherichia coli (E. coli) References: UniProt: P50053-2, UniProt: P50053*PLUS, ketohexokinase #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: 3.58 Å3/Da / Density % sol: 65.6 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 4.5 Details: 17% PEG 8k, 0.1M Na-Citrate, 0.2M Ammonium Sulfate, pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 17-BM / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 21, 2008 / Details: mirrors |
Radiation | Monochromator: double crystal mono Si(111) from accel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→44.96 Å / Num. all: 34751 / Num. obs: 31943 / % possible obs: 92 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.16 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 8.1 |
Reflection shell | Resolution: 2.5→2.58 Å / Redundancy: 5 % / Rmerge(I) obs: 0.637 / Mean I/σ(I) obs: 1.6 / Num. unique all: 3437 / % possible all: 91.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3NBV Resolution: 2.8→26.757 Å / SU ML: 0.52 / σ(F): 0.02 / σ(I): 0 / 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 / Bsol: 45.577 Å2 / ksol: 0.36 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.8→26.757 Å
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Refine LS restraints |
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LS refinement shell |
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