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- PDB-3c39: Crystal Structure of human phosphoglycerate kinase bound to 3-pho... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3c39 | ||||||
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Title | Crystal Structure of human phosphoglycerate kinase bound to 3-phosphoglycerate | ||||||
![]() | Phosphoglycerate kinase 1 | ||||||
![]() | TRANSFERASE / Two domain / kinase / beta sandwich / Acetylation / ATP-binding / Cytoplasm / Disease mutation / Glycolysis / Hereditary hemolytic anemia / Nucleotide-binding / Phosphoprotein / Polymorphism | ||||||
Function / homology | ![]() Manipulation of host energy metabolism / phosphoglycerate kinase / phosphoglycerate kinase activity / protein-disulfide reductase (NAD(P)H) activity / Gluconeogenesis / canonical glycolysis / Glycolysis / plasminogen activation / epithelial cell differentiation / negative regulation of angiogenesis ...Manipulation of host energy metabolism / phosphoglycerate kinase / phosphoglycerate kinase activity / protein-disulfide reductase (NAD(P)H) activity / Gluconeogenesis / canonical glycolysis / Glycolysis / plasminogen activation / epithelial cell differentiation / negative regulation of angiogenesis / gluconeogenesis / glycolytic process / ADP binding / cellular response to hypoxia / membrane raft / phosphorylation / extracellular space / extracellular exosome / ATP binding / membrane / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Arold, S.T. / Gondeau, C. / Lionne, C. / Chaloin, L. | ||||||
![]() | ![]() Title: Molecular basis for the lack of enantioselectivity of human 3-phosphoglycerate kinase Authors: Gondeau, C. / Chaloin, L. / Lallemand, P. / Roy, B. / Perigaud, C. / Barman, T. / Varga, A. / Vas, M. / Lionne, C. / Arold, S.T. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 170.2 KB | Display | ![]() |
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PDB format | ![]() | 132.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 441.4 KB | Display | ![]() |
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Full document | ![]() | 450.3 KB | Display | |
Data in XML | ![]() | 34.7 KB | Display | |
Data in CIF | ![]() | 51.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2zgvC ![]() 3c3aC ![]() 3c3bC ![]() 3c3cC ![]() 1vjcS C: citing same article ( S: Starting model for refinement |
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Similar 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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Components
#1: Protein | Mass: 44954.895 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2 Å3/Da / Density % sol: 38.6 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.3 Details: 2.6M NaKPO4, pH 8.3, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 27, 2007 |
Radiation | Monochromator: liquid nitrogen cooled channel-cut silicon monochromator Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→91.29 Å / Num. all: 44499 / Num. obs: 44499 / % possible obs: 77.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 1.9 % / Biso Wilson estimate: 21.22 Å2 / Rmerge(I) obs: 0.048 / Net I/σ(I): 14 |
Reflection shell | Resolution: 1.85→1.95 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 1.9 / Num. unique all: 3309 / % possible all: 50.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1VJC Resolution: 1.85→50.1 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.884 / SU B: 4.223 / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.23 / ESU R Free: 0.212 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.353 Å2
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Refinement step | Cycle: LAST / Resolution: 1.85→50.1 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.85→1.898 Å / Total num. of bins used: 20
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