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Open data
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Basic information
Entry | Database: PDB / ID: 8sw9 | ||||||
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Title | Plasmodium falciparum M17 (A460S) mutant | ||||||
![]() | Leucine aminopeptidase | ||||||
![]() | HYDROLASE / metallo-exopeptidase / M17 aminopeptidase / Leucine Aminopeptidase / malaria / aminopeptidase | ||||||
Function / homology | ![]() Hydrolases; Acting on peptide bonds (peptidases); Dipeptidases / leucyl aminopeptidase / metallodipeptidase activity / peptide catabolic process / metalloaminopeptidase activity / carboxypeptidase activity / peptidase activity / manganese ion binding / proteolysis / zinc ion binding ...Hydrolases; Acting on peptide bonds (peptidases); Dipeptidases / leucyl aminopeptidase / metallodipeptidase activity / peptide catabolic process / metalloaminopeptidase activity / carboxypeptidase activity / peptidase activity / manganese ion binding / proteolysis / zinc ion binding / identical protein binding / metal ion binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | McGowan, S. / Suraweera, C. / Drinkwater, N. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Characterisation of a novel antimalarial agent targeting haemaglobin digestion that shows cross-species reactivity and excellent in vivo properties. Authors: de Koning-Ward, T.F. / Drinkwater, N. / Edgar, R.C.S. / 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 | ![]() | 3.1 MB | Display | ![]() |
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PDB format | ![]() | 2.7 MB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 8svlC ![]() 8svmC C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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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: 58724.973 Da / Num. of mol.: 12 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: LAP, PF3D7_1446200 / Production host: ![]() ![]() References: UniProt: Q8IL11, leucyl aminopeptidase, Hydrolases; Acting on peptide bonds (peptidases); Dipeptidases |
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-Non-polymers , 5 types, 1129 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/CO3.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/1PE.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CO3.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/1PE.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-CO3 / #4: Chemical | ChemComp-SO4 / #5: Chemical | ChemComp-1PE / #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.46 Å3/Da / Density % sol: 50.03 % |
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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 / Ambient temp details: 10/11/2018 / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 10, 2018 |
Radiation | 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→49.57 Å / Num. obs: 213083 / % possible obs: 100 % / Redundancy: 7 % / CC1/2: 0.983 / Rmerge(I) obs: 0.373 / Rpim(I) all: 0.152 / Rrim(I) all: 0.403 / Χ2: 0.95 / Net I/σ(I): 3.8 / Num. measured all: 1485932 |
Reflection shell | Resolution: 2.6→2.64 Å / % possible obs: 100 % / Redundancy: 7 % / Rmerge(I) obs: 2.261 / Num. measured all: 72954 / Num. unique obs: 10487 / CC1/2: 0.575 / Rpim(I) all: 0.918 / Rrim(I) all: 2.442 / Χ2: 0.97 / Net I/σ(I) obs: 1.1 |
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Processing
Software |
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Refinement | Method to determine structure: ![]()
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.6→49.57 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: 89.6164 Å / Origin y: 56.0613 Å / Origin z: 78.2753 Å
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Refinement TLS group | Selection details: all |