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Yorodumi- PDB-4zx5: X-ray crystal structure of PfA-M1 in complex with hydroxamic acid... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4zx5 | ||||||
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Title | X-ray crystal structure of PfA-M1 in complex with hydroxamic acid-based inhibitor 10q | ||||||
Components | M1 family aminopeptidase | ||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / M1 ALANYL-AMINOPEPTIDASE / PROTEASE / INHIBITOR / HYDROXAMIC ACID / 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 / chloroplast / proteolysis / zinc ion binding ...symbiont-containing vacuole membrane / vacuolar lumen / Hydrolases; Acting on peptide bonds (peptidases); Aminopeptidases / food vacuole / dipeptidase activity / metalloaminopeptidase activity / aminopeptidase activity / chloroplast / proteolysis / zinc ion binding / membrane / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Plasmodium falciparum (malaria parasite P. falciparum) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å | ||||||
Authors | Drinkwater, N. / McGowan, S. | ||||||
Funding support | Australia, 1items
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Citation | Journal: Eur.J.Med.Chem. / Year: 2016 Title: Potent dual inhibitors of Plasmodium falciparum M1 and M17 aminopeptidases through optimization of S1 pocket interactions. Authors: Drinkwater, N. / Vinh, N.B. / Mistry, S.N. / Bamert, R.S. / Ruggeri, C. / Holleran, J.P. / Loganathan, S. / Paiardini, A. / Charman, S.A. / Powell, A.K. / Avery, V.M. / McGowan, S. / Scammells, P.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4zx5.cif.gz | 419.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4zx5.ent.gz | 340.2 KB | Display | PDB format |
PDBx/mmJSON format | 4zx5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4zx5_validation.pdf.gz | 743.1 KB | Display | wwPDB validaton report |
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Full document | 4zx5_full_validation.pdf.gz | 747.6 KB | Display | |
Data in XML | 4zx5_validation.xml.gz | 41.7 KB | Display | |
Data in CIF | 4zx5_validation.cif.gz | 65.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zx/4zx5 ftp://data.pdbj.org/pub/pdb/validation_reports/zx/4zx5 | HTTPS FTP |
-Related structure data
Related structure data | 4zw3C 4zw5C 4zw6C 4zw7C 4zw8C 4zx3C 4zx4C 4zx6C 4zx8C 4zx9C 4zy0C 4zy1C 4zy2C 4zyqC 3ebgS 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: 103760.719 Da / Num. of mol.: 1 / Fragment: UNP residues 195-1084 / Mutation: N213Q, N223Q, H378P, N501Q, N795Q, N1069Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum) Strain: isolate FcB1 / Columbia / Plasmid: PTRCHIS-2B / 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 , 6 types, 987 molecules
#2: Chemical | ChemComp-ZN / | ||||||
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#3: Chemical | ChemComp-4TM / | ||||||
#4: Chemical | #5: Chemical | #6: Chemical | ChemComp-GOL / | #7: 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: 2.31 Å3/Da / Density % sol: 46.87 % |
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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 pH 8.5, 0.2 M MgCl2 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Jul 26, 2014 |
Radiation | Monochromator: DOUBLE CRYSTAL SILICON 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→31.56 Å / Num. obs: 70857 / % possible obs: 100 % / Redundancy: 7.3 % / Biso Wilson estimate: 21.31 Å2 / Rmerge(I) obs: 0.166 / Net I/σ(I): 11.1 |
Reflection shell | Resolution: 1.95→1.99 Å / Redundancy: 7.3 % / Rmerge(I) obs: 1.276 / Mean I/σ(I) obs: 1.7 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3EBG Resolution: 1.95→31.56 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.82 / 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: 25.46 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.95→31.56 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: 92.3071 Å / Origin y: 113.0077 Å / Origin z: 10.2482 Å
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Refinement TLS group | Selection details: ALL |