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Yorodumi- PDB-3nc9: X-ray structure of ketohexokinase complexed with an indazole compound -
+Open data
-Basic information
Entry | Database: PDB / ID: 3nc9 | ||||||
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Title | X-ray structure of ketohexokinase complexed with an indazole compound | ||||||
Components | Ketohexokinase | ||||||
Keywords | TRANSFERASE/TRANSFERASE INHIBITOR / ketohexokinase / TRANSFERASE / 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 / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Abad, M.C. / Gibbs, A.C. / Spurlino, J.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 | 3nc9.cif.gz | 128 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3nc9.ent.gz | 99 KB | Display | PDB format |
PDBx/mmJSON format | 3nc9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3nc9_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 3nc9_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 3nc9_validation.xml.gz | 23.8 KB | Display | |
Data in CIF | 3nc9_validation.cif.gz | 32.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nc/3nc9 ftp://data.pdbj.org/pub/pdb/validation_reports/nc/3nc9 | HTTPS FTP |
-Related structure data
Related structure data | 3nbvSC 3nbwC 3nc2C 3ncaC 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: 3.56 Å3/Da / Density % sol: 65.42 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 4.5 Details: 17% PEG8k, 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: MAR CCD 165 mm / Detector: CCD / Date: Apr 3, 2009 / 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: 2.4→44.9 Å / Num. all: 38770 / Num. obs: 38469 / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.64 % / Rmerge(I) obs: 0.059 / Net I/σ(I): 10.6 |
Reflection shell | Resolution: 2.4→2.49 Å / Redundancy: 4.64 % / Mean I/σ(I) obs: 2.7 / Num. unique all: 3856 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 3NBV Resolution: 2.4→36.314 Å / SU ML: 0.43 / Isotropic thermal model: anisotropic / σ(F): 0.04 / 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: 64.121 Å2 / ksol: 0.389 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.4→36.314 Å
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Refine LS restraints |
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LS refinement shell |
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