[English] 日本語
Yorodumi- PDB-3qv7: Crystal structure of Leishmania mexicana pyruvate kinase(LmPYK)in... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3qv7 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of Leishmania mexicana pyruvate kinase(LmPYK)in complex with ponceau S and acid blue 25. | ||||||
Components | Pyruvate kinase | ||||||
Keywords | TRANSFERASE/TRANSFERASE INHIBITOR / PYRUVATE KINASE / GLYCOLYSIS / TIM Barrel / Sugar kinase / ADP/ATP binding / cytosol / TRANSFERASE-TRANSFERASE INHIBITOR complex | ||||||
Function / homology | Function and homology information pyruvate kinase / pyruvate kinase activity / potassium ion binding / cellular response to insulin stimulus / kinase activity / phosphorylation / magnesium ion binding / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | Leishmania mexicana (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | ||||||
Authors | Morgan, H.P. / Auld, D.S. / McNae, I.W. / Nowicki, M.W. / Michels, P.A.M. / Fothergill-Gilmore, L.A. / Walkinshaw, M.D. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2011 Title: The trypanocidal drug suramin and other trypan blue mimetics are inhibitors of pyruvate kinases and bind to the adenosine site. Authors: Morgan, H.P. / McNae, I.W. / Nowicki, M.W. / Zhong, W. / Michels, P.A. / Auld, D.S. / Fothergill-Gilmore, L.A. / Walkinshaw, M.D. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3qv7.cif.gz | 355.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3qv7.ent.gz | 289 KB | Display | PDB format |
PDBx/mmJSON format | 3qv7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3qv7_validation.pdf.gz | 2.1 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 3qv7_full_validation.pdf.gz | 2.1 MB | Display | |
Data in XML | 3qv7_validation.xml.gz | 67.2 KB | Display | |
Data in CIF | 3qv7_validation.cif.gz | 92.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qv/3qv7 ftp://data.pdbj.org/pub/pdb/validation_reports/qv/3qv7 | HTTPS FTP |
-Related structure data
Related structure data | 3pp7C 3qv6C 3qv8C 3qv9C 1pklS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
-Protein , 1 types, 4 molecules DABC
#1: Protein | Mass: 54467.934 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Leishmania mexicana (eukaryote) / Strain: BEL46 / Gene: PKY / Plasmid: pET3a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2 pLysS / References: UniProt: Q27686, pyruvate kinase |
---|
-Non-polymers , 5 types, 523 molecules
#2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-K / #4: Chemical | ChemComp-QV7 / #5: Chemical | ChemComp-QV8 / | #6: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
---|
-Sample preparation
Crystal | Density Matthews: 3.82 Å3/Da / Density % sol: 67.84 % |
---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.2 Details: 7-16% PEG 8,000, 20 mM TEA buffer (pH 7.2), 50 mM MgCl2, 100 mM KCl and 10-25% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 1 Å | ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Detector | Type: ADSC QUANTUM 315 / Detector: CCD | ||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||
Reflection | Resolution: 2.7→21.14 Å / Num. obs: 89354 / % possible obs: 100 % / Observed criterion σ(F): 2.7 / Observed criterion σ(I): 2.7 / Redundancy: 3.7 % / Biso Wilson estimate: 56.4 Å2 / Rmerge(I) obs: 0.123 / Rsym value: 0.144 / Net I/σ(I): 10.2 | ||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / % possible all: 100
|
-Processing
Software | Name: REFMAC / Version: 5.5.0109 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1PKL Resolution: 2.7→21.14 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.903 / SU B: 10.317 / SU ML: 0.206 / Cross valid method: THROUGHOUT / ESU R Free: 0.277 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 45.246 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.7→21.14 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.7→2.769 Å / Total num. of bins used: 20
|