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Yorodumi- PDB-4cku: Three dimensional structure of plasmepsin II in complex with hydr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4cku | ||||||
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Title | Three dimensional structure of plasmepsin II in complex with hydroxyethylamine-based inhibitor | ||||||
Components | PLASMEPSIN-2 | ||||||
Keywords | HYDROLASE / MALARIA / DRUG DESIGN | ||||||
Function / homology | Function and homology information cytostome / plasmepsin II / acquisition of nutrients from host / vacuolar lumen / food vacuole / vacuolar membrane / aspartic-type endopeptidase activity / proteolysis Similarity search - Function | ||||||
Biological species | PLASMODIUM FALCIPARUM (malaria parasite P. falciparum) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å | ||||||
Authors | Tars, K. / Leitans, J. / Jaudzems, K. | ||||||
Citation | Journal: Acs Med.Chem.Lett. / Year: 2014 Title: Plasmepsin Inhibitory Activity and Structure-Guided Optimization of a Potent Hydroxyethylamine-Based Antimalarial Hit. Authors: Jaudzems, K. / Tars, K. / Maurops, G. / Ivdra, N. / Otikovs, M. / Leitans, J. / Kanepe-Lapsa, I. / Domraceva, I. / Mutule, I. / Trapencieris, P. / Blackman, M.J. / Jirgensons, A. | ||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4cku.cif.gz | 411.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4cku.ent.gz | 339.1 KB | Display | PDB format |
PDBx/mmJSON format | 4cku.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4cku_validation.pdf.gz | 2.5 MB | Display | wwPDB validaton report |
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Full document | 4cku_full_validation.pdf.gz | 2.5 MB | Display | |
Data in XML | 4cku_validation.xml.gz | 84.8 KB | Display | |
Data in CIF | 4cku_validation.cif.gz | 117.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ck/4cku ftp://data.pdbj.org/pub/pdb/validation_reports/ck/4cku | HTTPS FTP |
-Related structure data
Related structure data | 2bjuS 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 36909.617 Da / Num. of mol.: 6 / Fragment: PLASMEPSIN-2, RESIDUES 125-453 Source method: isolated from a genetically manipulated source Source: (gene. exp.) PLASMODIUM FALCIPARUM (malaria parasite P. falciparum) Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P46925, plasmepsin II #2: Chemical | ChemComp-P2F / #3: 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: 2.29 Å3/Da / Density % sol: 46.27 % / Description: NONE |
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Crystal grow | Method: vapor diffusion, sitting drop / pH: 4.5 Details: 0.1M CITRIC ACID, PH 4.5, 0.3M AMMONIUM ACETATE, 25% PEG 3350, PROTEIN 10 MG/ML, VAPOR DIFFUSION, SITTING DROP, TIME 2-4 WEEKS. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: MAX II / Beamline: I911-3 / Wavelength: 1 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Dec 18, 2011 / Details: MIRRORS |
Radiation | Monochromator: DOUBLE SI CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→30 Å / Num. obs: 166099 / % possible obs: 98 % / Redundancy: 2.6 % / Biso Wilson estimate: 16.852 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 9.2 |
Reflection shell | Resolution: 1.85→1.95 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.28 / Mean I/σ(I) obs: 3.5 / % possible all: 99.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2BJU Resolution: 1.85→29.98 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.939 / SU B: 2.819 / SU ML: 0.086 / Cross valid method: THROUGHOUT / ESU R: 0.129 / ESU R Free: 0.129 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
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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: 24.732 Å2
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Refinement step | Cycle: LAST / Resolution: 1.85→29.98 Å
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Refine LS restraints |
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