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- PDB-6ka6: Crystal structure of plasmodium lysyl-tRNA synthetase in complex ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6ka6 | ||||||
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Title | Crystal structure of plasmodium lysyl-tRNA synthetase in complex with a cladosporin derivative 1 | ||||||
![]() | Lysine--tRNA ligase | ||||||
![]() | LIGASE / Inhibitor / Complex | ||||||
Function / homology | ![]() ATP:ADP adenylyltransferase activity / lysine-tRNA ligase / lysine-tRNA ligase activity / lysyl-tRNA aminoacylation / diadenosine tetraphosphate biosynthetic process / aminoacyl-tRNA synthetase multienzyme complex / positive regulation of macrophage activation / tRNA binding / mitochondrion / extracellular space ...ATP:ADP adenylyltransferase activity / lysine-tRNA ligase / lysine-tRNA ligase activity / lysyl-tRNA aminoacylation / diadenosine tetraphosphate biosynthetic process / aminoacyl-tRNA synthetase multienzyme complex / positive regulation of macrophage activation / tRNA binding / mitochondrion / extracellular space / ATP binding / nucleus / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Zhou, J. / Fang, P. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Atomic Resolution Analyses of Isocoumarin Derivatives for Inhibition of Lysyl-tRNA Synthetase. Authors: Zhou, J. / Zheng, L. / Hei, Z. / Li, W. / Wang, J. / Yu, B. / Fang, P. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 833.2 KB | Display | ![]() |
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PDB format | ![]() | 685.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.6 MB | Display | ![]() |
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Full document | ![]() | 1.6 MB | Display | |
Data in XML | ![]() | 84.3 KB | Display | |
Data in CIF | ![]() | 123.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6kabC ![]() 6kbfC ![]() 6kcnC ![]() 6kctC ![]() 4ycvS S: Starting model for refinement C: citing same article ( |
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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: 59781.133 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: isolate NF54 / Gene: PFNF54_04763 / Production host: ![]() ![]() #2: Chemical | ChemComp-D4O / ( #3: Chemical | ChemComp-GOL / #4: Chemical | ChemComp-LYS / #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.51 Å3/Da / Density % sol: 50.99 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / Details: tri-sodium citrate, PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 14, 2019 | ||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||
Radiation wavelength | Wavelength: 0.97853 Å / Relative weight: 1 | ||||||||||||||||||
Reflection | Resolution: 1.89→38.68 Å / Num. obs: 164813 / % possible obs: 88.8 % / Redundancy: 3.5 % / Biso Wilson estimate: 24.25 Å2 / Rmerge(I) obs: 0.122 / Net I/σ(I): 5 | ||||||||||||||||||
Reflection shell |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4YCV Resolution: 1.891→32.597 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.92 / Phase error: 26.85
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 111.11 Å2 / Biso mean: 33.6835 Å2 / Biso min: 14.73 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.891→32.597 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10
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Refinement TLS params. | Method: refined / Origin x: 1.5933 Å / Origin y: 12.9705 Å / Origin z: 23.0346 Å
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Refinement TLS group |
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