[English] 日本語
Yorodumi- PDB-5hfu: Crystal Structure of Human Hexokinase 2 with cmpd 27, a 2-amido-6... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5hfu | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure of Human Hexokinase 2 with cmpd 27, a 2-amido-6-benzenesulfonamide glucosamine | ||||||
Components | Hexokinase-2 | ||||||
Keywords | TRANSFERASE/TRANSFERASE INHIBITOR / metabolism / inhibitor complex / TRANSFERASE-TRANSFERASE INHIBITOR complex | ||||||
Function / homology | Function and homology information negative regulation of mitochondrial membrane permeability / hexokinase activity / maintenance of protein location in mitochondrion / regulation of glucose import / establishment of protein localization to mitochondrion / positive regulation of autophagy of mitochondrion in response to mitochondrial depolarization / hexokinase / fructokinase activity / carbohydrate phosphorylation / glucokinase activity ...negative regulation of mitochondrial membrane permeability / hexokinase activity / maintenance of protein location in mitochondrion / regulation of glucose import / establishment of protein localization to mitochondrion / positive regulation of autophagy of mitochondrion in response to mitochondrial depolarization / hexokinase / fructokinase activity / carbohydrate phosphorylation / glucokinase activity / glucose 6-phosphate metabolic process / D-glucose binding / fructose 6-phosphate metabolic process / canonical glycolysis / Glycolysis / intracellular glucose homeostasis / apoptotic mitochondrial changes / negative regulation of reactive oxygen species metabolic process / lactation / sarcoplasmic reticulum / cellular response to leukemia inhibitory factor / response to ischemia / glycolytic process / positive regulation of angiogenesis / glucose metabolic process / mitochondrial outer membrane / response to hypoxia / intracellular membrane-bounded organelle / centrosome / mitochondrion / ATP binding / membrane / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.923 Å | ||||||
Authors | Campobasso, N. / Zhao, B. / Smallwood, A. | ||||||
Citation | Journal: Acs Med.Chem.Lett. / Year: 2016 Title: Discovery of a Novel 2,6-Disubstituted Glucosamine Series of Potent and Selective Hexokinase 2 Inhibitors. Authors: Lin, H. / Zeng, J. / Xie, R. / Schulz, M.J. / Tedesco, R. / Qu, J. / Erhard, K.F. / Mack, J.F. / Raha, K. / Rendina, A.R. / Szewczuk, L.M. / Kratz, P.M. / Jurewicz, A.J. / Cecconie, T. / ...Authors: Lin, H. / Zeng, J. / Xie, R. / Schulz, M.J. / Tedesco, R. / Qu, J. / Erhard, K.F. / Mack, J.F. / Raha, K. / Rendina, A.R. / Szewczuk, L.M. / Kratz, P.M. / Jurewicz, A.J. / Cecconie, T. / Martens, S. / McDevitt, P.J. / Martin, J.D. / Chen, S.B. / Jiang, Y. / Nickels, L. / Schwartz, B.J. / Smallwood, A. / Zhao, B. / Campobasso, N. / Qian, Y. / Briand, J. / Rominger, C.M. / Oleykowski, C. / Hardwicke, M.A. / Luengo, J.I. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5hfu.cif.gz | 355.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5hfu.ent.gz | 284.3 KB | Display | PDB format |
PDBx/mmJSON format | 5hfu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5hfu_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 5hfu_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 5hfu_validation.xml.gz | 64 KB | Display | |
Data in CIF | 5hfu_validation.cif.gz | 86.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hf/5hfu ftp://data.pdbj.org/pub/pdb/validation_reports/hf/5hfu | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 103102.508 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HK2 / Production host: Escherichia coli (E. coli) / References: UniProt: P52789, hexokinase #2: Chemical | ChemComp-603 / ~{ #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
---|
-Sample preparation
Crystal | Density Matthews: 2.82 Å3/Da / Density % sol: 56.35 % |
---|---|
Crystal grow | Temperature: 296 K / Method: vapor diffusion / pH: 6 Details: protein: 10mgs/mL in 50mM TrisHCL pH = 7.5, 250mM NaCl, 2mM DTT, 2mM MgCl2 Well solution: 0.1M Na Citrate pH = 6, 16 % PEG3350, 10 % Ethylene glycol Cryo: 20 % ethylene glycol in well PH range: 5 - 6 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.9787 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 9, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9787 Å / Relative weight: 1 |
Reflection | Resolution: 2.92→113.64 Å / Num. obs: 49230 / % possible obs: 99.8 % / Redundancy: 3.8 % / Net I/σ(I): 11.2 |
-Processing
Software |
| ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.923→113.64 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.26 / Stereochemistry target values: ML
| ||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.923→113.64 Å
| ||||||||||||||||||||||||
Refine LS restraints |
|