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- PDB-1bg3: RAT BRAIN HEXOKINASE TYPE I COMPLEX WITH GLUCOSE AND INHIBITOR GL... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1bg3 | ||||||
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Title | RAT BRAIN HEXOKINASE TYPE I COMPLEX WITH GLUCOSE AND INHIBITOR GLUCOSE-6-PHOSPHATE | ||||||
![]() | HEXOKINASE | ||||||
![]() | HEXOKINASE / PHOSPHOTRANSFERASE | ||||||
Function / homology | ![]() response to ketamine / Glycolysis / regulation of anion channel activity / response to brassinosteroid / hexokinase activity / sperm principal piece / maintenance of protein location in mitochondrion / mannokinase activity / establishment of protein localization to mitochondrion / hexokinase ...response to ketamine / Glycolysis / regulation of anion channel activity / response to brassinosteroid / hexokinase activity / sperm principal piece / maintenance of protein location in mitochondrion / mannokinase activity / establishment of protein localization to mitochondrion / hexokinase / positive regulation of cytokine production involved in immune response / fructokinase activity / carbohydrate phosphorylation / glucokinase activity / mannose metabolic process / glucose 6-phosphate metabolic process / peptidoglycan binding / D-glucose binding / fructose 6-phosphate metabolic process / intracellular glucose homeostasis / positive regulation of interleukin-1 beta production / caveola / response to ischemia / glycolytic process / peptidyl-threonine phosphorylation / cilium / peptidyl-tyrosine phosphorylation / peptidyl-serine phosphorylation / mitochondrial outer membrane / protein autophosphorylation / response to hypoxia / protein kinase activity / inflammatory response / membrane raft / protein phosphorylation / innate immune response / protein-containing complex binding / negative regulation of apoptotic process / ATP hydrolysis activity / protein-containing complex / mitochondrion / ATP binding / identical protein binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Mulichak, A.M. / Garavito, R.M. | ||||||
![]() | ![]() Title: The structure of mammalian hexokinase-1. Authors: Mulichak, A.M. / Wilson, J.E. / Padmanabhan, K. / Garavito, R.M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 351 KB | Display | ![]() |
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PDB format | ![]() | 281.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.6 MB | Display | ![]() |
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Full document | ![]() | 1.6 MB | Display | |
Data in XML | ![]() | 66 KB | Display | |
Data in CIF | ![]() | 91.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.999992, 0.001479, -0.003776), Vector: Details | ALTHOUGH ENZYME IS ACTIVE AS A MONOMER, DIMERIZATION OCCURS AT HIGH PROTEIN CONCENTRATION, PARTICULARLY IN THE PRESENCE OF THE INHIBITOR G6P | |
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Components
#1: Protein | Mass: 102545.156 Da / Num. of mol.: 2 / Source method: isolated from a natural source Details: BOTH MONOMERS HAVE TWO SMALL BREAKS AT KNOWN OR LIKELY TRYPSIN CLEAVAGE SITES. ALTHOUGH ENZYME IS ACTIVE AS A MONOMER, DIMERIZATION OCCURS AT HIGH PROTEIN CONCENTRATION, PARTICULARLY IN THE ...Details: BOTH MONOMERS HAVE TWO SMALL BREAKS AT KNOWN OR LIKELY TRYPSIN CLEAVAGE SITES. ALTHOUGH ENZYME IS ACTIVE AS A MONOMER, DIMERIZATION OCCURS AT HIGH PROTEIN CONCENTRATION, PARTICULARLY IN THE PRESENCE OF THE INHIBITOR G6P Source: (natural) ![]() ![]() #2: Sugar | ChemComp-BGC / #3: Sugar | ChemComp-G6P / #4: Chemical | ChemComp-CA / | #5: Water | ChemComp-HOH / | Compound details | BOTH MONOMERS HAVE TWO SMALL BREAKS AT KNOWN OR LIKELY TRYPSIN CLEAVAGE SITES. | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.5 Å3/Da / Density % sol: 55 % | ||||||||||||||||||||||||
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Crystal grow | pH: 7 / Details: pH 7.0 | ||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 153 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Aug 1, 1997 / Details: MSC FOCUSSING MIRRORS |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Highest resolution: 2.8 Å / Num. obs: 54454 / % possible obs: 79 % / Observed criterion σ(I): 1 / Redundancy: 2 % / Rmerge(I) obs: 0.076 / Net I/σ(I): 8 |
Reflection shell | Resolution: 2.8→3 Å / Rmerge(I) obs: 0.17 / Mean I/σ(I) obs: 3 / % possible all: 59 |
Reflection shell | *PLUS % possible obs: 59 % |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Starting model: HEXOKINASE FROM SCHISTOSOMA MANSONI Resolution: 2.8→20 Å / Cross valid method: THROUGHOUT / σ(F): 2
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Displacement parameters | Biso mean: 20 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.8→2.9 Å / Total num. of bins used: 8
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Xplor file |
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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