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Yorodumi- PDB-4ycw: Crystal structure of cladosporin in complex with plasmodium like ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4ycw | |||||||||
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Title | Crystal structure of cladosporin in complex with plasmodium like human lysyl-tRNA synthetase mutant | |||||||||
Components |
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Keywords | ligase/ligase inhibitor / Inhibitor / Complex / LysRS / cladosporin / ligase-ligase inhibitor complex | |||||||||
Function / homology | Function and homology information ATP:ADP adenylyltransferase activity / type II pneumocyte differentiation / basophil activation involved in immune response / positive regulation of inflammatory response to antigenic stimulus / Mitochondrial tRNA aminoacylation / lysine-tRNA ligase / lysine-tRNA ligase activity / lysyl-tRNA aminoacylation / Selenoamino acid metabolism / diadenosine tetraphosphate biosynthetic process ...ATP:ADP adenylyltransferase activity / type II pneumocyte differentiation / basophil activation involved in immune response / positive regulation of inflammatory response to antigenic stimulus / Mitochondrial tRNA aminoacylation / lysine-tRNA ligase / lysine-tRNA ligase activity / lysyl-tRNA aminoacylation / Selenoamino acid metabolism / diadenosine tetraphosphate biosynthetic process / aminoacyl-tRNA synthetase multienzyme complex / Cytosolic tRNA aminoacylation / positive regulation of macrophage activation / tRNA processing / amino acid binding / response to X-ray / ERK1 and ERK2 cascade / positive regulation of protein ubiquitination / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / protein-containing complex assembly / tRNA binding / molecular adaptor activity / protein ubiquitination / mitochondrial matrix / translation / negative regulation of cell population proliferation / apoptotic process / positive regulation of DNA-templated transcription / protein homodimerization activity / mitochondrion / extracellular space / ATP binding / membrane / identical protein binding / nucleus / plasma membrane / cytosol Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å | |||||||||
Authors | Fang, P. / Wang, J. / Guo, M. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Chem.Biol. / Year: 2015 Title: Structural Basis for Specific Inhibition of tRNA Synthetase by ATP Competitive Inhibitor Authors: Fang, P. / Han, H. / Wang, J. / Chen, K. / Chen, X. / Guo, M. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ycw.cif.gz | 799.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ycw.ent.gz | 662.4 KB | Display | PDB format |
PDBx/mmJSON format | 4ycw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yc/4ycw ftp://data.pdbj.org/pub/pdb/validation_reports/yc/4ycw | HTTPS FTP |
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-Related structure data
Related structure data | 3bjuS S: Starting model for refinement |
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Similar structure data |
-Links
-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: 59201.102 Da / Num. of mol.: 4 / Fragment: unp residues 98-609 / Mutation: P300T, Q321V, T337S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: KARS, KIAA0070 / Production host: Escherichia coli (E. coli) / References: UniProt: Q15046, lysine-tRNA ligase #2: Protein/peptide | Mass: 4911.680 Da / Num. of mol.: 4 / Fragment: unp residues 1-36 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: AIMP2, JTV1, PRO0992 / Production host: Escherichia coli (E. coli) / References: UniProt: Q13155 #3: Chemical | ChemComp-LYS / #4: Chemical | ChemComp-KRS / #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.28 Å3/Da / Density % sol: 46.09 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: PEG 4000, MES |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 15, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→40 Å / Num. obs: 89884 / % possible obs: 93.5 % / Redundancy: 2.1 % / Biso Wilson estimate: 49.62 Å2 / Rmerge(I) obs: 0.087 / Net I/σ(I): 6.9 |
Reflection shell | Resolution: 2.9→3 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.453 / % possible all: 90.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3BJU Resolution: 2.9→35.45 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.77 / Phase error: 29.08 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 62.48 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.9→35.45 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -0.1343 Å / Origin y: 14.3847 Å / Origin z: 38.8135 Å
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Refinement TLS group | Selection details: ALL |