[English] 日本語
Yorodumi- PDB-1bg3: RAT BRAIN HEXOKINASE TYPE I COMPLEX WITH GLUCOSE AND INHIBITOR GL... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1bg3 | ||||||
---|---|---|---|---|---|---|---|
Title | RAT BRAIN HEXOKINASE TYPE I COMPLEX WITH GLUCOSE AND INHIBITOR GLUCOSE-6-PHOSPHATE | ||||||
Components | HEXOKINASE | ||||||
Keywords | HEXOKINASE / PHOSPHOTRANSFERASE | ||||||
Function / homology | Function and homology information response to ketamine / Glycolysis / regulation of anion channel activity / response to brassinosteroid / hexokinase activity / sperm principal piece / mannokinase activity / maintenance of protein location in mitochondrion / positive regulation of cytokine production involved in immune response / establishment of protein localization to mitochondrion ...response to ketamine / Glycolysis / regulation of anion channel activity / response to brassinosteroid / hexokinase activity / sperm principal piece / mannokinase activity / maintenance of protein location in mitochondrion / positive regulation of cytokine production involved in immune response / establishment of protein localization to mitochondrion / hexokinase / fructokinase activity / carbohydrate phosphorylation / glucokinase activity / mannose metabolic process / glucose 6-phosphate metabolic process / peptidoglycan binding / glucose binding / fructose 6-phosphate metabolic process / intracellular glucose homeostasis / positive regulation of interleukin-1 beta production / response to ischemia / caveola / 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 | Rattus norvegicus (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Mulichak, A.M. / Garavito, R.M. | ||||||
Citation | Journal: Nat.Struct.Biol. / Year: 1998 Title: The structure of mammalian hexokinase-1. Authors: Mulichak, A.M. / Wilson, J.E. / Padmanabhan, K. / Garavito, R.M. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1bg3.cif.gz | 350.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1bg3.ent.gz | 281.1 KB | Display | PDB format |
PDBx/mmJSON format | 1bg3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bg/1bg3 ftp://data.pdbj.org/pub/pdb/validation_reports/bg/1bg3 | HTTPS FTP |
---|
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
| ||||||||
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 | |
-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) Rattus norvegicus (Norway rat) / Organ: BRAIN / Tissue: BRAIN / References: UniProt: P05708, hexokinase #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. | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.5 Å3/Da / Density % sol: 55 % | ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | pH: 7 / Details: pH 7.0 | ||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 153 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418 |
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 % |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: HEXOKINASE FROM SCHISTOSOMA MANSONI Resolution: 2.8→20 Å / Cross valid method: THROUGHOUT / σ(F): 2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→20 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.8→2.9 Å / Total num. of bins used: 8
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
|