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- PDB-6ee2: X-ray crystal structure of Pf-M17 in complex with inhibitor 6i an... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6ee2 | |||||||||
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Title | X-ray crystal structure of Pf-M17 in complex with inhibitor 6i and regulatory zinc ion | |||||||||
![]() | Pf-M17 | |||||||||
![]() | hydrolase/hydrolase inhibitor / M17 LEUCYL-AMINOPEPTIDASE / PROTEASE / INHIBITOR / HYDROXAMIC ACID / hydrolase-hydrolase inhibitor complex | |||||||||
Function / homology | ![]() | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Drinkwater, N. / McGowan, S. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Hydroxamic Acid Inhibitors Provide Cross-Species Inhibition of Plasmodium M1 and M17 Aminopeptidases. Authors: Vinh, N.B. / Drinkwater, N. / Malcolm, T.R. / Kassiou, M. / Lucantoni, L. / Grin, P.M. / Butler, G.S. / Duffy, S. / Overall, C.M. / Avery, V.M. / Scammells, P.J. / McGowan, S. | |||||||||
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 | ![]() | 1 MB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 3.9 MB | Display | ![]() |
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Full document | ![]() | 3.9 MB | Display | |
Data in XML | ![]() | 250.7 KB | Display | |
Data in CIF | ![]() | 357.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6ea1C ![]() 6ea2C ![]() 6eaaC ![]() 6eabC ![]() 6ee3C ![]() 6ee4C ![]() 6ee6C ![]() 6eedC ![]() 6eeeC 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: 58439.629 Da / Num. of mol.: 12 / Fragment: UNP residues 85-605 / Mutation: N152Q,N515Q,N563Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: PFNF135_05834 / Production host: ![]() ![]() |
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-Non-polymers , 8 types, 4107 molecules ![](data/chem/img/CO3.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/J1V.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/1PE.gif)
![](data/chem/img/DMS.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/J1V.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/1PE.gif)
![](data/chem/img/DMS.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-CO3 / #3: Chemical | ChemComp-ZN / #4: Chemical | ChemComp-J1V / #5: Chemical | ChemComp-SO4 / #6: Chemical | ChemComp-1PE / #7: Chemical | ChemComp-DMS / #8: Chemical | #9: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.52 Å3/Da / Density % sol: 51.28 % / Mosaicity: 0.12 ° |
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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: Mar 19, 2016 | ||||||||||||||||||||||||
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: 2.1→44.77 Å / Num. obs: 409865 / % possible obs: 99.6 % / Redundancy: 4.9 % / Biso Wilson estimate: 18.91 Å2 / CC1/2: 0.957 / Rmerge(I) obs: 0.514 / Rpim(I) all: 0.235 / Rrim(I) all: 0.568 / Net I/σ(I): 4.1 | ||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 132.65 Å2 / Biso mean: 20.5723 Å2 / Biso min: 4.17 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.1→44.77 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30
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