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Open data
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Basic information
Entry | Database: PDB / ID: 2vgi | ||||||||||||
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Title | HUMAN ERYTHROCYTE PYRUVATE KINASE: R486W MUTANT | ||||||||||||
![]() | PYRUVATE KINASE ISOZYMES R/L | ||||||||||||
![]() | TRANSFERASE / GLYCOLYSIS | ||||||||||||
Function / homology | ![]() pyruvate kinase complex / pyruvate biosynthetic process / SARS-CoV-1-host interactions / ChREBP activates metabolic gene expression / pyruvate kinase / pyruvate kinase activity / Pyruvate metabolism / monosaccharide binding / response to metal ion / Glycolysis ...pyruvate kinase complex / pyruvate biosynthetic process / SARS-CoV-1-host interactions / ChREBP activates metabolic gene expression / pyruvate kinase / pyruvate kinase activity / Pyruvate metabolism / monosaccharide binding / response to metal ion / Glycolysis / response to ATP / Regulation of gene expression in beta cells / potassium ion binding / response to glucose / response to cAMP / cellular response to epinephrine stimulus / response to nutrient / glycolytic process / cellular response to insulin stimulus / kinase activity / response to hypoxia / magnesium ion binding / extracellular exosome / ATP binding / cytosol / cytoplasm Similarity search - Function | ||||||||||||
Biological species | ![]() | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Valentini, G. / Chiarelli, L. / Fortin, R. / Dolzan, M. / Galizzi, A. / Abraham, D.J. / Wang, C. / Bianchi, P. / Zanella, A. / Mattevi, A. | ||||||||||||
![]() | ![]() Title: Structure and Function of Human Erythrocyte Pyruvate Kinase. Molecular Basis of Nonspherocytic Hemolytic Anemia. Authors: Valentini, G. / Chiarelli, L.R. / Fortin, R. / Dolzan, M. / Galizzi, A. / Abraham, D.J. / Wang, C. / Bianchi, P. / Zanella, A. / Mattevi, A. | ||||||||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 9-STRANDED BARREL THIS IS REPRESENTED BY A 10-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BA" AND "CA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "DA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 7-STRANDED BARREL THIS IS REPRESENTED BY A 8-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 338.3 KB | Display | ![]() |
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PDB format | ![]() | 267.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 2vgbSC ![]() 2vgfC ![]() 2vggC C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Assembly
Deposited unit | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
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Components
#1: Protein | Mass: 57003.340 Da / Num. of mol.: 4 / Fragment: RESIDUES 47-574 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Sugar | ChemComp-FBP / #3: Chemical | ChemComp-PGA / #4: Chemical | ChemComp-K / #5: Chemical | ChemComp-MN / Compound details | ENGINEERED RESIDUE IN CHAIN A, ARG 486 TO TRP ENGINEERED RESIDUE IN CHAIN B, ARG 486 TO TRP ...ENGINEERED | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 50.35 % / Description: NONE |
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Crystal grow | pH: 6.4 / Details: pH 6.4 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD / Date: Jun 10, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→20 Å / Num. obs: 42512 / % possible obs: 89 % / Observed criterion σ(I): 0 / Redundancy: 1.8 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 7.2 |
Reflection shell | Resolution: 2.9→3 Å / Redundancy: 1.4 % / Rmerge(I) obs: 0.28 / Mean I/σ(I) obs: 2.4 / % possible all: 68.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2VGB Resolution: 2.87→20 Å / Cor.coef. Fo:Fc: 0.889 / Cor.coef. Fo:Fc free: 0.833 / SU B: 54.254 / SU ML: 0.502 / TLS residual ADP flag: UNVERIFIED / Cross valid method: THROUGHOUT / ESU R Free: 0.569 / 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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 2 Å2
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Refinement step | Cycle: LAST / Resolution: 2.87→20 Å
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Refine LS restraints |
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