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Yorodumi- PDB-5eu9: Structure of Human Enolase 2 in complex with ((3S,5S)-1,5-dihydro... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5eu9 | |||||||||
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Title | Structure of Human Enolase 2 in complex with ((3S,5S)-1,5-dihydroxy-3-methyl-2-oxopyrrolidin-3-yl)phosphonic acid | |||||||||
Components | Gamma-enolase | |||||||||
Keywords | LYASE/LYASE INHIBITOR / enolase gamma / glycolysis / neuron specific enolase / carbohydrate metabolism / LYASE-LYASE INHIBITOR complex | |||||||||
Function / homology | Function and homology information phosphopyruvate hydratase / phosphopyruvate hydratase complex / phosphopyruvate hydratase activity / Gluconeogenesis / canonical glycolysis / Glycolysis / photoreceptor inner segment / gluconeogenesis / glycolytic process / perikaryon ...phosphopyruvate hydratase / phosphopyruvate hydratase complex / phosphopyruvate hydratase activity / Gluconeogenesis / canonical glycolysis / Glycolysis / photoreceptor inner segment / gluconeogenesis / glycolytic process / perikaryon / magnesium ion binding / extracellular space / extracellular exosome / membrane / plasma membrane / cytosol Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.047 Å | |||||||||
Authors | Leonard, P.G. / Muller, F.L. | |||||||||
Funding support | United States, 2items
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Citation | Journal: To be Published Title: SF2312, a natural phosphonate inhibitor of Enolase Authors: Leonard, P.G. / Maxwell, D. / Satani, N. / Peng, Z. / Link, T. / Lee, G. / Bosajou, A. / Sun, D. / Lin, Y.E. / DiFrancesco, M.E. / Czako, B. / Wang, Y.A. / Bornmann, W. / DePhinho, R.A. / Muller, F.L. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5eu9.cif.gz | 705.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5eu9.ent.gz | 580.5 KB | Display | PDB format |
PDBx/mmJSON format | 5eu9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/eu/5eu9 ftp://data.pdbj.org/pub/pdb/validation_reports/eu/5eu9 | HTTPS FTP |
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-Related structure data
Related structure data | 4zcwS 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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2 |
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3 |
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4 |
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Unit cell |
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-Components
#1: Protein | Mass: 48149.270 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ENO2 / Plasmid: pJL-H6 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): Rosetta2 plysS / References: UniProt: P09104, phosphopyruvate hydratase #2: Chemical | ChemComp-MG / #3: Chemical | ChemComp-5TX / (( #4: Chemical | ChemComp-PGE / #5: 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: 2.34 Å3/Da / Density % sol: 47.39 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 100 mM Bis-Tris, pH 6.5, 200 mM ammonium acetate, 18-22% w/v PEG3350, soak overnight in 2 mM compound, 100 mM Bis-Tris, 200 mM ammonium acetate, 32% w/v PEG3350, pH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11587 Å | |||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 31, 2015 | |||||||||||||||||||||||||||
Radiation | Monochromator: double flat crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.11587 Å / Relative weight: 1 | |||||||||||||||||||||||||||
Reflection | Redundancy: 6.7 % / Number: 1464678 / Rmerge(I) obs: 0.2 / D res high: 2.05 Å / D res low: 89.93 Å / Num. obs: 217213 / % possible obs: 97.6 / Rejects: 506 | |||||||||||||||||||||||||||
Diffraction reflection shell |
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Reflection | Resolution: 2.05→89.93 Å / Num. obs: 217213 / % possible obs: 97.6 % / Redundancy: 6.7 % / Biso Wilson estimate: 18.15 Å2 / CC1/2: 0.988 / Rmerge(I) obs: 0.2 / Rpim(I) all: 0.083 / Net I/σ(I): 6.4 / Num. measured all: 1464678 / Scaling rejects: 506 | |||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 4ZCW Resolution: 2.047→89.928 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.28 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 90.34 Å2 / Biso mean: 21.4287 Å2 / Biso min: 4.98 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.047→89.928 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14
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