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Yorodumi- PDB-3nbv: X-ray Structure of Ketohexokinase in complex with AMP-PNP and fructose -
+Open data
-Basic information
Entry | Database: PDB / ID: 3nbv | ||||||
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Title | X-ray Structure of Ketohexokinase in complex with AMP-PNP and fructose | ||||||
Components | Ketohexokinase | ||||||
Keywords | TRANSFERASE/TRANSFERASE INHIBITOR / ketohexokinase / TRANSFERASE / TRANSFERASE-TRANSFERASE INHIBITOR complex | ||||||
Function / homology | Function and homology information Essential fructosuria / ketohexokinase / Fructose catabolism / ketohexokinase activity / regulation of glycogen metabolic process / response to sucrose / response to fructose / fructose metabolic process / response to zinc ion / response to glucose ...Essential fructosuria / ketohexokinase / Fructose catabolism / ketohexokinase activity / 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: 2.3 Å | ||||||
Authors | Abad, M.C. / Gibbs, A.C. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2010 Title: Electron density guided fragment-based lead discovery of ketohexokinase inhibitors. Authors: Gibbs, A.C. / Abad, M.C. / Zhang, X. / Tounge, B.A. / Lewandowski, F.A. / Struble, G.T. / Sun, W. / Sui, Z. / Kuo, L.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3nbv.cif.gz | 131 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3nbv.ent.gz | 100.4 KB | Display | PDB format |
PDBx/mmJSON format | 3nbv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3nbv_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 3nbv_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 3nbv_validation.xml.gz | 25.3 KB | Display | |
Data in CIF | 3nbv_validation.cif.gz | 34.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nb/3nbv ftp://data.pdbj.org/pub/pdb/validation_reports/nb/3nbv | HTTPS FTP |
-Related structure data
Related structure data | 3nbwC 3nc2C 3nc9C 3ncaC 2hlzS 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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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: Sugar | ChemComp-FRU / | #4: Chemical | ChemComp-SO4 / | #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: 3.58 Å3/Da / Density % sol: 65.65 % |
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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: 200 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 5, 2007 / Details: mirror |
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: 2.2→50 Å / Num. obs: 49441 / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.7 % / Rmerge(I) obs: 0.071 / Rsym value: 0.066 / Net I/σ(I): 18.9 |
Reflection shell | Resolution: 2.2→2.28 Å / Redundancy: 4.6 % / Mean I/σ(I) obs: 2.85 / Num. unique all: 4843 / % possible all: 97.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2HLZ Resolution: 2.3→41.041 Å / SU ML: 0.32 / Isotropic thermal model: anisotropic / σ(F): 1.34 / 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: 62.236 Å2 / ksol: 0.4 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.3→41.041 Å
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Refine LS restraints |
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LS refinement shell |
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