[English] 日本語
Yorodumi- PDB-5yie: Crystal Structure of KNI-10742 bound Plasmepsin II (PMII) from Pl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5yie | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure of KNI-10742 bound Plasmepsin II (PMII) from Plasmodium falciparum | ||||||
Components | Plasmepsin II | ||||||
Keywords | HYDROLASE / Plasmepsin / Plasmepsin II / KNI-10742 / 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 / MOLECULAR REPLACEMENT / Resolution: 2.1 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 | 5yie.cif.gz | 150.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5yie.ent.gz | 124 KB | Display | PDB format |
PDBx/mmJSON format | 5yie.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yi/5yie ftp://data.pdbj.org/pub/pdb/validation_reports/yi/5yie | HTTPS FTP |
---|
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 36769.562 Da / Num. of mol.: 1 / Fragment: UNP residues 127-453 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Plasmodium falciparum (isolate 3D7) (eukaryote) Gene: PF14_0077, PF3D7_1408000 / Production host: Enterobacteria phage L1 (virus) / References: UniProt: Q8I6V3, plasmepsin II | ||||||
---|---|---|---|---|---|---|---|
#2: Chemical | #3: Chemical | ChemComp-8VF / ( | #4: Chemical | ChemComp-NA / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.79 Å3/Da / Density % sol: 55.9 % |
---|---|
Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.1 M HEPES pH 7.5, 1.4 M sodium citrate tribasic dihydrate |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54182 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Oct 30, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54182 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→40 Å / Num. obs: 23705 / % possible obs: 100 % / Redundancy: 7.4 % / Rmerge(I) obs: 0.065 / Net I/σ(I): 17.4 |
Reflection shell | Resolution: 2.1→2.2 Å / Redundancy: 7.3 % / Rmerge(I) obs: 1.25 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 3089 / % possible all: 99.9 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→38 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.959 / SU B: 10.825 / SU ML: 0.148 / Cross valid method: THROUGHOUT / ESU R: 0.189 / ESU R Free: 0.168 / 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: 61.757 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.1→38 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|