+Open data
-Basic information
Entry | Database: PDB / ID: 5zh2 | ||||||
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Title | CRYSTAL STRUCTURE OF PfKRS WITH INHIBITOR CLADO-5 | ||||||
Components | Lysine-tRNA ligase | ||||||
Keywords | LIGASE / KRS / LIGASE-LIGASE INHIBITOR COMPLEX | ||||||
Function / homology | Function and homology information 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 | Plasmodium falciparum NF54 (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.66 Å | ||||||
Authors | Babbar, P. / Malhotra, N. / Sharma, M. / Harlos, K. / Reddy, D.S. / Manickam, Y. / Sharma, A. | ||||||
Citation | Journal: J. Med. Chem. / Year: 2018 Title: Specific Stereoisomeric Conformations Determine the Drug Potency of Cladosporin Scaffold against Malarial Parasite Authors: Das, P. / Babbar, P. / Malhotra, N. / Sharma, M. / Jachak, G.R. / Gonnade, R.G. / Shanmugam, D. / Harlos, K. / Yogavel, M. / Sharma, A. / Reddy, D.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5zh2.cif.gz | 380.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5zh2.ent.gz | 308.9 KB | Display | PDB format |
PDBx/mmJSON format | 5zh2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5zh2_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 5zh2_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 5zh2_validation.xml.gz | 33.7 KB | Display | |
Data in CIF | 5zh2_validation.cif.gz | 46.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zh/5zh2 ftp://data.pdbj.org/pub/pdb/validation_reports/zh/5zh2 | HTTPS FTP |
-Related structure data
Related structure data | 5zh3C 5zh4C 5zh5C 4pg3S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 58706.934 Da / Num. of mol.: 2 / Fragment: UNK residues 15-621 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Plasmodium falciparum NF54 (eukaryote) / Gene: PFNF54_04763 / Plasmid: PETM-41 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: W7JP72, lysine-tRNA ligase #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-CL / #5: Chemical | ChemComp-MPO / | |
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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: 2.58 Å3/Da / Density % sol: 52.24 % |
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Crystal grow | Temperature: 283 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.1M Carboxylic acids, 0.1M Sodium HEPES/MOPS, 25%(v/v) MPD, 25% PEG 1000, 25%(w/v) PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 24, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 2.66→47.06 Å / Num. obs: 35718 / % possible obs: 99.8 % / Redundancy: 12.9 % / CC1/2: 0.9935 / Net I/σ(I): 8.5 |
Reflection shell | Resolution: 2.66→2.71 Å / Redundancy: 13.85 % / Mean I/σ(I) obs: 1.38 / Num. unique obs: 1744 / CC1/2: 0.5079 / % possible all: 100 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4PG3 Resolution: 2.66→47.05 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.908 / SU B: 27.326 / SU ML: 0.253 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.789 / ESU R Free: 0.328 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 127.88 Å2 / Biso mean: 48.003 Å2 / Biso min: 26.21 Å2
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Refinement step | Cycle: final / Resolution: 2.66→47.05 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.66→2.729 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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