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- PDB-4zx9: X-ray crystal structure of PfA-M17 in complex with hydroxamic aci... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4zx9 | ||||||
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Title | X-ray crystal structure of PfA-M17 in complex with hydroxamic acid-based inhibitor 10b | ||||||
![]() | Probable M17 family aminopeptidase | ||||||
![]() | HYDROLASE/HYDROLASE INHIBITOR / M17 LEUCYL-AMINOPEPTIDASE / PROTEASE / INHIBITOR / HYDROXAMIC ACID / HYDROLASE-HYDROLASE INHIBITOR complex | ||||||
Function / homology | ![]() leucyl aminopeptidase / metalloaminopeptidase activity / manganese ion binding / proteolysis / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Drinkwater, N. / McGowan, S. | ||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 1.2 MB | Display | ![]() |
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PDB format | ![]() | 972.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4zw3C ![]() 4zw5C ![]() 4zw6C ![]() 4zw7C ![]() 4zw8C ![]() 4zx3C ![]() 4zx4C ![]() 4zx5C ![]() 4zx6C ![]() 4zx8C ![]() 4zy0C ![]() 4zy1C ![]() 4zy2C ![]() 4zyqC ![]() 3kqzS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
-Protein , 1 types, 12 molecules ABCDEFGHIJKL
#1: Protein | Mass: 57982.230 Da / Num. of mol.: 12 / Fragment: UNP residues 84-605 / Mutation: D152N,D515N,D516N Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: isolate FcB1 / Columbia / Plasmid: PTRCHIS-2B / Production host: ![]() ![]() |
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-Non-polymers , 8 types, 1394 molecules ![](data/chem/img/4TK.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/CO3.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/1PE.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/DMS.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/CO3.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/1PE.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/DMS.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-4TK / #3: Chemical | ChemComp-ZN / #4: Chemical | ChemComp-CO3 / #5: Chemical | ChemComp-GOL / #6: Chemical | ChemComp-1PE / #7: Chemical | ChemComp-SO4 / #8: Chemical | ChemComp-DMS / #9: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.56 Å3/Da / Density % sol: 51.94 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 40% (v/v) PEG 400, 0.1 M Tris pH 8.5, 0.2 M Li2SO4 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 17, 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: 2.6→48.48 Å / Num. obs: 195787 / % possible obs: 90.7 % / Redundancy: 7.7 % / Biso Wilson estimate: 28.44 Å2 / CC1/2: 0.983 / Rmerge(I) obs: 0.284 / Rpim(I) all: 0.097 / Net I/σ(I): 5.4 / Num. measured all: 1499465 / Scaling rejects: 1011 | |||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3KQZ Resolution: 2.6→46.742 Å / FOM work R set: 0.739 / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.45 / 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 max: 98.54 Å2 / Biso mean: 32.61 Å2 / Biso min: 8.7 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.6→46.742 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30
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