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Yorodumi- PDB-5xm7: Crystal structure of Plasmodium falciparum aminopeptidase N in co... -
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-Basic information
Entry | Database: PDB / ID: 5xm7 | ||||||
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Title | Crystal structure of Plasmodium falciparum aminopeptidase N in complex with (S)-2-((2S,3R)-3-amino-2-hydroxy-4-phenylbutanamido)-N-hydroxy-4-methylpentanamide | ||||||
Components | M1 family aminopeptidase | ||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / Aminopeptidase / M1-class / 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 (malaria parasite P. falciparum) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.96 Å | ||||||
Authors | Marapaka, A.K. / Zhang, Y. / Addlagatta, A. | ||||||
Citation | Journal: Chin.Chem.Lett. / Year: 2022 Title: Development of peptidomimetic hydroxamates as PfA-M1 and PfA-M17 dual inhibitors: Biological evaluation and structural characterization by cocrystallization Authors: Marapaka, A.K. / Sankoju, P. / Zhang, G. / Ding, Y. / Ma, C. / Pillalamarri, V. / Sudhakar, P. / Reddi, B. / Sijwali, P.S. / Zhang, Y. / Addlagatta, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5xm7.cif.gz | 211.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5xm7.ent.gz | 160.4 KB | Display | PDB format |
PDBx/mmJSON format | 5xm7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xm/5xm7 ftp://data.pdbj.org/pub/pdb/validation_reports/xm/5xm7 | HTTPS FTP |
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-Related structure data
Related structure data | 5y1kC 5y1qC 5y1tC 4x2uS 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 106291.477 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 195-1085 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum) Production host: Escherichia coli (E. coli) References: UniProt: O96935, Hydrolases; Acting on peptide bonds (peptidases); Aminopeptidases |
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-Non-polymers , 5 types, 396 molecules
#2: Chemical | ChemComp-ZN / | ||||||
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#3: Chemical | #4: Chemical | ChemComp-GOL / #5: Chemical | ChemComp-89X / ( | #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: 2.2 Å3/Da / Density % sol: 44.09 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 0.1M Tris, or trisaminomethane pH8.5, 0.2M magnesium chloride, 24%PEG2000 PH range: 7.5-8.5 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RIGAKU AFC-5R / Detector: CCD / Date: May 22, 2016 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.96→25 Å / Num. obs: 66352 / % possible obs: 100 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.082 / Χ2: 1.058 / Net I/σ(I): 19.8 / Num. measured all: 424528 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement | ||||||
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Phasing MR | R rigid body: 0.378
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4X2U Resolution: 1.96→24.976 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.948 / WRfactor Rfree: 0.2422 / WRfactor Rwork: 0.1852 / FOM work R set: 0.8485 / SU B: 3.554 / SU ML: 0.102 / SU R Cruickshank DPI: 0.1679 / SU Rfree: 0.1546 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.168 / ESU R Free: 0.155 / 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 max: 93.53 Å2 / Biso mean: 31.71 Å2 / Biso min: 5.85 Å2
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Refinement step | Cycle: final / Resolution: 1.96→24.976 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.96→2.011 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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