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Yorodumi- PDB-6p2d: Structure of mouse ketohexokinase-C in complex with fructose and ADP -
+Open data
-Basic information
Entry | Database: PDB / ID: 6p2d | |||||||||
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Title | Structure of mouse ketohexokinase-C in complex with fructose and ADP | |||||||||
Components | Ketohexokinase | |||||||||
Keywords | TRANSFERASE / beta-clasp / sugar kinase / PfKB family / KHK / ketohexokinase / fructose / ADP | |||||||||
Function / homology | Function and homology information glycolytic process through fructose-1-phosphate / Fructose catabolism / fructose catabolic process to hydroxyacetone phosphate and glyceraldehyde-3-phosphate / ketohexokinase / ketohexokinase activity / regulation of glycogen metabolic process / response to sucrose / response to fructose / fructose metabolic process / response to zinc ion ...glycolytic process through fructose-1-phosphate / Fructose catabolism / fructose catabolic process to hydroxyacetone phosphate and glyceraldehyde-3-phosphate / ketohexokinase / 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 / ATP binding / nucleus / cytoplasm Similarity search - Function | |||||||||
Biological species | Mus musculus (house mouse) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.79 Å | |||||||||
Authors | Gasper, W.C. / Allen, K.N. / Tolan, D.R. | |||||||||
Funding support | 1items
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Citation | Journal: ACTA CRYSTALLOGR.,SECT.D / Year: 2024 Title: Michaelis-like complex of mouse ketohexokinase isoform C Authors: Gasper, W.C. / Gardner, S. / Ross, A. / Oppelt, S.A. / Allen, K.N. / Tolan, D.R. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6p2d.cif.gz | 84.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6p2d.ent.gz | 59.9 KB | Display | PDB format |
PDBx/mmJSON format | 6p2d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6p2d_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 6p2d_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 6p2d_validation.xml.gz | 17.2 KB | Display | |
Data in CIF | 6p2d_validation.cif.gz | 26.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p2/6p2d ftp://data.pdbj.org/pub/pdb/validation_reports/p2/6p2d | HTTPS FTP |
-Related structure data
Related structure data | 3q92S 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 34827.434 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Khk, mCG_23498 / Plasmid: pPB1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0J9YU79, UniProt: P97328*PLUS |
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#2: Chemical | ChemComp-ADP / |
#3: Sugar | ChemComp-FRU / |
#4: Chemical | ChemComp-NO3 / |
#5: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.79 Å3/Da / Density % sol: 31.32 % |
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Crystal grow | Temperature: 290.15 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 1.2 M Ammonium Citrate Tribasic, 20% glycerol, 1.3 M KNO3, 100 mM MgCl2, 220 mM fructose, and 52 mM ADP |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.54 Å |
Detector | Type: Bruker Platinum 135 / Detector: CCD / Date: Dec 22, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 1.79→37.96 Å / Num. obs: 23632 / % possible obs: 97 % / Redundancy: 1.88 % / Biso Wilson estimate: 9.33 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.14 / Rrim(I) all: 0.15 / Net I/σ(I): 14.3 |
Reflection shell | Resolution: 1.79→1.86 Å / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 6.4 / Num. unique obs: 2058 / CC1/2: 0.95 / % possible all: 74 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3Q92 Resolution: 1.79→37.96 Å / Cross valid method: THROUGHOUT
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Refinement step | Cycle: LAST / Resolution: 1.79→37.96 Å
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