[English] 日本語
Yorodumi- PDB-7ve0: Crystal Structure of Ritonavir bound Plasmepsin II (PMII) from Pl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7ve0 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure of Ritonavir bound Plasmepsin II (PMII) from Plasmodium falciparum | ||||||
Components | Plasmepsin II | ||||||
Keywords | HYDROLASE / Inhibitor / Protease / Peptidomimetic / HIV-1 protease inhibitor / peptidase / hemoglobin degrader | ||||||
Function / homology | Function and homology information MHC class II antigen presentation / hemoglobin catabolic process / cytostome / plasmepsin II / Neutrophil degranulation / vacuolar lumen / food vacuole / vacuolar membrane / aspartic-type endopeptidase activity / proteolysis Similarity search - Function | ||||||
Biological species | Plasmodium falciparum (malaria parasite P. falciparum) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Mishra, V. / Rathore, I. / Bhaumik, P. | ||||||
Funding support | India, 1items
| ||||||
Citation | Journal: Curr Res Struct Biol / Year: 2024 Title: Inhibition of Plasmodium falciparum plasmepsins by drugs targeting HIV-1 protease: A way forward for antimalarial drug discovery. Authors: Mishra, V. / Deshmukh, A. / Rathore, I. / Chakraborty, S. / Patankar, S. / Gustchina, A. / Wlodawer, A. / Yada, R.Y. / Bhaumik, P. #1: Journal: Biorxiv / Year: 2023 Title: Molecular insights into the inhibition of plasmepsins by HIV-1 protease inhibitors: Implications for antimalarial drug discovery. Authors: Mishra, V. / Rathore, I. / Bhaumik, P. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 7ve0.cif.gz | 300.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7ve0.ent.gz | 246.6 KB | Display | PDB format |
PDBx/mmJSON format | 7ve0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ve/7ve0 ftp://data.pdbj.org/pub/pdb/validation_reports/ve/7ve0 | HTTPS FTP |
---|
-Related structure data
Related structure data | 7ve2C 5yicS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 37113.926 Da / Num. of mol.: 2 / Mutation: H320Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Plasmodium falciparum (isolate 3D7) (eukaryote) Strain: isolate 3D7 / Gene: PF3D7_1408000 / Plasmid: pET32b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta-gami B(DE3)pLysS / References: UniProt: Q8I6V3, plasmepsin II #2: Chemical | #3: Chemical | ChemComp-CPS / #4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.76 Å3/Da / Density % sol: 55.48 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 2.5 M sodium formate, pH 7.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: RRCAT INDUS-2 / Beamline: PX-BL21 / Wavelength: 0.9795 Å |
Detector | Type: RAYONIX MX225HE / Detector: CCD / Date: Sep 25, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→39.89 Å / Num. obs: 61329 / % possible obs: 95.9 % / Redundancy: 2.89 % / Biso Wilson estimate: 41.24 Å2 / CC1/2: 0.99 / Net I/σ(I): 16.16 |
Reflection shell | Resolution: 1.9→2 Å / Redundancy: 2.73 % / Mean I/σ(I) obs: 1.84 / Num. unique obs: 8741 / CC1/2: 0.65 / % possible all: 96.6 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5YIC Resolution: 1.9→39.89 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.929 / SU B: 11.327 / SU ML: 0.172 / Cross valid method: THROUGHOUT / ESU R: 0.188 / ESU R Free: 0.167 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 51.907 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 1.9→39.89 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|