+Open data
-Basic information
Entry | Database: PDB / ID: 8svm | ||||||
---|---|---|---|---|---|---|---|
Title | Plasmodium falciparum M17 aminopeptidase bound to MMV1557817 | ||||||
Components | Leucine aminopeptidase | ||||||
Keywords | HYDROLASE / metallo-exopeptidase / protease inhibitor / malaria / Plasmodium / M17 aminopeptidase | ||||||
Function / homology | Function and homology information 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 / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Plasmodium falciparum (malaria parasite P. falciparum) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | McGowan, S. / Drinkwater, N. | ||||||
Funding support | Australia, 1items
| ||||||
Citation | Journal: Mbio / Year: 2024 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 8svm.cif.gz | 2.3 MB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb8svm.ent.gz | 1.9 MB | Display | PDB format |
PDBx/mmJSON format | 8svm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8svm_validation.pdf.gz | 3.7 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 8svm_full_validation.pdf.gz | 3.7 MB | Display | |
Data in XML | 8svm_validation.xml.gz | 236.7 KB | Display | |
Data in CIF | 8svm_validation.cif.gz | 329.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sv/8svm ftp://data.pdbj.org/pub/pdb/validation_reports/sv/8svm | HTTPS FTP |
-Related structure data
Related structure data | 8svlC 8sw9C C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
-Protein , 1 types, 12 molecules ABCDEFGHIJKL
#1: Protein | Mass: 58708.973 Da / Num. of mol.: 12 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum) Gene: LAP, PF3D7_1446200 / Production host: Escherichia coli (E. coli) References: UniProt: Q8IL11, leucyl aminopeptidase, Hydrolases; Acting on peptide bonds (peptidases); Dipeptidases |
---|
-Non-polymers , 6 types, 3121 molecules
#2: Chemical | ChemComp-CO3 / #3: Chemical | ChemComp-ZN / #4: Chemical | ChemComp-WRC / Mass: 394.388 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C20H21F3N2O3 / Feature type: SUBJECT OF INVESTIGATION #5: Chemical | ChemComp-1PE / #6: Chemical | ChemComp-SO4 / #7: Water | ChemComp-HOH / | |
---|
-Details
Has ligand of interest | Y |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.53 Å3/Da / Density % sol: 51.33 % |
---|---|
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 / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 23, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→49 Å / Num. obs: 306939 / % possible obs: 97.6 % / Redundancy: 3 % / CC1/2: 0.931 / Rmerge(I) obs: 0.331 / Rpim(I) all: 0.223 / Rrim(I) all: 0.402 / Net I/σ(I): 3.9 |
Reflection shell | Resolution: 2.3→2.34 Å / % possible obs: 96.3 % / Redundancy: 2.9 % / Rmerge(I) obs: 2.129 / Num. measured all: 43972 / Num. unique obs: 14962 / CC1/2: 0.15 / Rpim(I) all: 1.483 / Rrim(I) all: 2.614 / Net I/σ(I) obs: 1.5 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→49 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 30.13 / Stereochemistry target values: ML
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→49 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Origin x: 176.5625 Å / Origin y: 234.4452 Å / Origin z: 194.2267 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group | Selection details: all |