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- PDB-7qzu: Structure of liver pyruvate kinase in complex with anthraquinone ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7qzu | ||||||
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Title | Structure of liver pyruvate kinase in complex with anthraquinone derivative 47 | ||||||
![]() | PKL | ||||||
![]() | TRANSFERASE / Pyruvate kinase / active site / inhibition | ||||||
Function / homology | 1,6-di-O-phosphono-beta-D-fructofuranose / Chem-I4L / : / OXALATE ION![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Lulla, A. / Foller, A. / Nain-Perez, A. / Grotli, M. / Brear, P. / Hyvonen, M. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Anthraquinone derivatives as ADP-competitive inhibitors of liver pyruvate kinase. Authors: Nain-Perez, A. / Foller Fuchtbauer, A. / Haversen, L. / Lulla, A. / Gao, C. / Matic, J. / Monjas, L. / Rodriguez, A. / Brear, P. / Kim, W. / Hyvonen, M. / Boren, J. / Mardinoglu, A. / Uhlen, M. / Grotli, M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 712 KB | Display | ![]() |
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PDB format | ![]() | 587.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 5.4 MB | Display | ![]() |
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Full document | ![]() | 5.5 MB | Display | |
Data in XML | ![]() | 140.8 KB | Display | |
Data in CIF | ![]() | 203.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5sc8C ![]() 5sc9C ![]() 5scaC ![]() 5scbC ![]() 5sccC ![]() 5scdC ![]() 5sceC ![]() 5scfC ![]() 5scgC ![]() 5schC ![]() 5sciC ![]() 5scjC ![]() 5sckC ![]() 5sclC ![]() 5sdtC ![]() 7qdnSC S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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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
-Protein / Sugars , 2 types, 16 molecules ABCDEFGH![](data/chem/img/FBP.gif)
![](data/chem/img/FBP.gif)
#1: Protein | Mass: 48285.379 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Sugar | ChemComp-FBP / |
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-Non-polymers , 5 types, 2553 molecules ![](data/chem/img/OXL.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/K.gif)
![](data/chem/img/I4L.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/K.gif)
![](data/chem/img/I4L.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-OXL / #4: Chemical | ChemComp-MG / #5: Chemical | ChemComp-K / #6: Chemical | ChemComp-I4L / ( #7: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.86 Å3/Da / Density % sol: 56.92 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 100 mM HEPES/MOPS, 10% PEG8000, 20% ethylene glycol, 10 mM phenylalanine, 20 mM sodium oxalate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 16, 2019 | |||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9587 Å / Relative weight: 1 | |||||||||||||||||||||||||||
Reflection | Resolution: 1.964→188.725 Å / Num. obs: 237404 / % possible obs: 94.9 % / Redundancy: 6.9 % / CC1/2: 0.998 / Rmerge(I) obs: 0.11 / Rpim(I) all: 0.045 / Net I/σ(I): 11.3 | |||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 7QDN Resolution: 1.964→188.72 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.936 / SU R Cruickshank DPI: 0.212 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.22 / SU Rfree Blow DPI: 0.172 / SU Rfree Cruickshank DPI: 0.17 Details: HYDROGENS WERE FULLY REFINED WITH ZERO OCCUPANCY AT NUCLEAR POSITION. REFINEMENT NOTES. NUMBER OF REFINEMENT NOTES : 1 NOTE 1 : IDEAL-DIST CONTACT TERM CONTACT SETUP. ALL ATOMS HAVE CCP4 ATOM TYPE FROM LIBRARY
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Displacement parameters | Biso max: 116.14 Å2 / Biso mean: 38.32 Å2 / Biso min: 12.95 Å2
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Refine analyze | Luzzati coordinate error obs: 0.27 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.964→188.72 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.964→2.08 Å / Rfactor Rfree error: 0
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