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Yorodumi- PDB-4k5m: Phosphonic Arginine Mimetics as Inhibitors of the M1 Aminopeptida... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4k5m | ||||||
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Title | Phosphonic Arginine Mimetics as Inhibitors of the M1 Aminopeptidases from Plasmodium falciparum | ||||||
Components | M1 family aminopeptidase | ||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / M1 Alanyl-Aminopeptidase / Protease / HYDROLASE-HYDROLASE INHIBITOR complex | ||||||
Function / homology | Function and homology information symbiont-containing vacuole membrane / vacuolar lumen / Hydrolases; Acting on peptide bonds (peptidases); Aminopeptidases / food vacuole / dipeptidase activity / metalloaminopeptidase activity / aminopeptidase activity / proteolysis / zinc ion binding / membrane ...symbiont-containing vacuole membrane / vacuolar lumen / Hydrolases; Acting on peptide bonds (peptidases); Aminopeptidases / food vacuole / dipeptidase activity / metalloaminopeptidase activity / aminopeptidase activity / proteolysis / zinc ion binding / membrane / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Plasmodium falciparum FcB1/Columbia (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å | ||||||
Authors | McGowan, S. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2013 Title: Synthesis and Structure-Activity Relationships of Phosphonic Arginine Mimetics as Inhibitors of the M1 and M17 Aminopeptidases from Plasmodium falciparum. Authors: Kannan Sivaraman, K. / Paiardini, A. / Sienczyk, M. / Ruggeri, C. / Oellig, C.A. / Dalton, J.P. / Scammells, P.J. / Drag, M. / McGowan, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4k5m.cif.gz | 390.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4k5m.ent.gz | 310.6 KB | Display | PDB format |
PDBx/mmJSON format | 4k5m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4k5m_validation.pdf.gz | 458 KB | Display | wwPDB validaton report |
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Full document | 4k5m_full_validation.pdf.gz | 467.1 KB | Display | |
Data in XML | 4k5m_validation.xml.gz | 44 KB | Display | |
Data in CIF | 4k5m_validation.cif.gz | 70.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k5/4k5m ftp://data.pdbj.org/pub/pdb/validation_reports/k5/4k5m | HTTPS FTP |
-Related structure data
Related structure data | 4k3nC 4k5lC 4k5nC 4k5oC 4k5pC 3ebhS C: citing same article (ref.) 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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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 104833.969 Da / Num. of mol.: 1 / Fragment: unp residues 195-1085 / Mutation: N213Q, N223Q, H378P, N501Q, N795Q, N1069QQ Source method: isolated from a genetically manipulated source Source: (gene. exp.) Plasmodium falciparum FcB1/Columbia (eukaryote) Production host: Escherichia coli (E. coli) / Strain (production host): BL21 References: UniProt: O96935, Hydrolases; Acting on peptide bonds (peptidases); Aminopeptidases |
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-Non-polymers , 5 types, 1154 molecules
#2: Chemical | ChemComp-ZN / | ||||||
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#3: Chemical | #4: Chemical | #5: Chemical | ChemComp-1OV / [( | #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.34 Å3/Da / Density % sol: 47.5 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 22% (v/v) PEG 8000, 10% (v/v) glycerol, 0.1 M Tris, 0.2 M MgCl2, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.95467 Å |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Feb 19, 2010 |
Radiation | Monochromator: Double Silicon Crystal 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.95467 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→80.32 Å / Num. all: 1433526 / Num. obs: 99259 / % possible obs: 98.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 1.75→1.84 Å / % possible all: 92.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 3ebh Resolution: 1.75→80.26 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.943 / SU B: 4.891 / SU ML: 0.072 / Cross valid method: THROUGHOUT / ESU R: 0.108 / ESU R Free: 0.11 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.44 Å2
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Refinement step | Cycle: LAST / Resolution: 1.75→80.26 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.747→1.792 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 17.676 Å / Origin y: 4.131 Å / Origin z: 10.217 Å
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Refinement TLS group |
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