[English] 日本語
Yorodumi- PDB-5yic: Crystal Structure of KNI-10333 bound Plasmepsin II (PMII) from Pl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5yic | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure of KNI-10333 bound Plasmepsin II (PMII) from Plasmodium falciparum | ||||||
Components | Plasmepsin II | ||||||
Keywords | HYDROLASE / Plasmepsin / Plasmepsin II / KNI-10333 / Aspartic Protease / Plasmodium falciparum / Drug Development / inhibitor | ||||||
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: Febs J. / Year: 2018 Title: Deciphering the mechanism of potent peptidomimetic inhibitors targeting plasmepsins - biochemical and structural insights. Authors: Mishra, V. / Rathore, I. / Arekar, A. / Sthanam, L.K. / Xiao, H. / Kiso, Y. / Sen, S. / Patankar, S. / Gustchina, A. / Hidaka, K. / Wlodawer, A. / Yada, R.Y. / Bhaumik, P. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5yic.cif.gz | 152 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5yic.ent.gz | 125.1 KB | Display | PDB format |
PDBx/mmJSON format | 5yic.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yi/5yic ftp://data.pdbj.org/pub/pdb/validation_reports/yi/5yic | HTTPS FTP |
---|
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 36856.641 Da / Num. of mol.: 1 / Fragment: UNP residues 126-453 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum) Gene: PF14_0077, PF3D7_1408000 / Production host: Enterobacteria phage L1 (virus) / References: UniProt: Q8I6V3, plasmepsin II | ||
---|---|---|---|
#2: Chemical | ChemComp-8VO / ( | ||
#3: Chemical | ChemComp-CPS / | ||
#4: Chemical | ChemComp-GOL / #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.73 Å3/Da / Density % sol: 54.96 % |
---|---|
Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 0.2 M lithium sulfate, 1.26 M ammonium sulfate, 0.1 M Tris pH 8.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.9537 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 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: 1.9→40 Å / Num. obs: 31284 / % possible obs: 99.7 % / Redundancy: 5.3 % / Rmerge(I) obs: 0.056 / Net I/σ(I): 16.6 |
Reflection shell | Resolution: 1.9→2 Å / Redundancy: 5.2 % / Rmerge(I) obs: 1.23 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 4420 / % possible all: 99.7 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→37.65 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.949 / SU B: 7.929 / SU ML: 0.118 / Cross valid method: THROUGHOUT / ESU R: 0.142 / ESU R Free: 0.14 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 48.159 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 1.9→37.65 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|