[English] 日本語
Yorodumi- PDB-6eee: X-ray crystal structure of Pf-M17 in complex with inhibitor (6k) ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6eee | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | X-ray crystal structure of Pf-M17 in complex with inhibitor (6k) and regulatory zinc ion | |||||||||
Components | M17 LEUCYL-AMINOPEPTIDASE | |||||||||
Keywords | hydrolase/hydrolase inhibitor / M17 LEUCYL-AMINOPEPTIDASE / PROTEASE / INHIBITOR / HYDROXAMIC ACID / hydrolase-hydrolase inhibitor complex | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Plasmodium falciparum (malaria parasite P. falciparum) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | |||||||||
Authors | Drinkwater, N. / McGowan, S. | |||||||||
Funding support | Australia, 2items
| |||||||||
Citation | Journal: J. Med. Chem. / Year: 2019 Title: Hydroxamic Acid Inhibitors Provide Cross-Species Inhibition of Plasmodium M1 and M17 Aminopeptidases. Authors: Vinh, N.B. / Drinkwater, N. / Malcolm, T.R. / Kassiou, M. / Lucantoni, L. / Grin, P.M. / Butler, G.S. / Duffy, S. / Overall, C.M. / Avery, V.M. / Scammells, P.J. / McGowan, S. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6eee.cif.gz | 1.2 MB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6eee.ent.gz | 997.7 KB | Display | PDB format |
PDBx/mmJSON format | 6eee.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ee/6eee ftp://data.pdbj.org/pub/pdb/validation_reports/ee/6eee | HTTPS FTP |
---|
-Related structure data
Related structure data | 6ea1C 6ea2C 6eaaC 6eabC 6ee2C 6ee3C 6ee4C 6ee6C 6eedC C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
-Protein , 1 types, 12 molecules ABCDEFGHIJKL
#1: Protein | Mass: 57564.648 Da / Num. of mol.: 12 / Mutation: N68Q, N431Q, N462Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Plasmodium falciparum (isolate HB3) (eukaryote) Strain: isolate HB3 / Gene: PFHG_04072 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0L7KHE6 |
---|
-Non-polymers , 9 types, 2310 molecules
#2: Chemical | ChemComp-J4V / ( #3: Chemical | ChemComp-CO3 / #4: Chemical | ChemComp-ZN / #5: Chemical | ChemComp-SO4 / #6: Chemical | ChemComp-DMS / #7: Chemical | ChemComp-1PE / #8: Chemical | ChemComp-EDO / #9: Chemical | ChemComp-2PE / | #10: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.56 Å3/Da / Density % sol: 51.99 % |
---|---|
Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / Details: 30% PEG400, 0.2M Li2SO4, 0.1M Tris pH 8 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 6, 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→48.88 Å / Num. obs: 311885 / % possible obs: 99.8 % / Redundancy: 5.8 % / Biso Wilson estimate: 27.8 Å2 / Rmerge(I) obs: 0.253 / Net I/σ(I): 5.9 |
Reflection shell | Resolution: 2.3→2.34 Å / Redundancy: 5.8 % / Rmerge(I) obs: 1.512 / % possible all: 99.5 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→48.17 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 29.94 / Stereochemistry target values: ML
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.45 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→48.17 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|