[English] 日本語
Yorodumi- PDB-6sbq: The crystal structure of PfA-M1 in complex with 7-amino-4-phenyl-... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6sbq | |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | The crystal structure of PfA-M1 in complex with 7-amino-4-phenyl-5,7,8,9-tetrahydrobenzocyclohepten-6-one | |||||||||||||||
Components | M1-family alanyl aminopeptidase | |||||||||||||||
Keywords | HYDROLASE / M1 AMINOPEPTIDASE | |||||||||||||||
Function / homology | Function and homology information symbiont-containing vacuole membrane / vacuolar lumen / Hydrolases; Acting on peptide bonds (peptidases); Aminopeptidases / food vacuole / dipeptidase activity / metalloaminopeptidase activity / aminopeptidase activity / proteolysis / zinc ion binding / membrane ...symbiont-containing vacuole membrane / vacuolar lumen / Hydrolases; Acting on peptide bonds (peptidases); Aminopeptidases / food vacuole / dipeptidase activity / metalloaminopeptidase activity / aminopeptidase activity / proteolysis / zinc ion binding / membrane / nucleus / cytoplasm Similarity search - Function | |||||||||||||||
Biological species | Plasmodium falciparum (malaria parasite P. falciparum) | |||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.33 Å | |||||||||||||||
Authors | Salomon, E. / Schmitt, M. / Mouray, E. / McEwen, A.G. / Torchy, M. / Poussin-Courmontagne, P. / Alavi, S. / Tarnus, C. / Cavarelli, J. / Florent, I. / Albrecht, S. | |||||||||||||||
Funding support | France, 4items
| |||||||||||||||
Citation | Journal: Bioorg.Chem. / Year: 2020 Title: Aminobenzosuberone derivatives as PfA-M1 inhibitors: Molecular recognition and antiplasmodial evaluation. Authors: Salomon, E. / Schmitt, M. / Mouray, E. / McEwen, A.G. / Bounaadja, L. / Torchy, M. / Poussin-Courmontagne, P. / Alavi, S. / Tarnus, C. / Cavarelli, J. / Florent, I. / Albrecht, S. | |||||||||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6sbq.cif.gz | 638.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6sbq.ent.gz | 530.4 KB | Display | PDB format |
PDBx/mmJSON format | 6sbq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sb/6sbq ftp://data.pdbj.org/pub/pdb/validation_reports/sb/6sbq | HTTPS FTP |
---|
-Related structure data
Related structure data | 6sbrC 4x2uS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 107617.758 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Plasmodium falciparum (isolate 3D7) (eukaryote) Gene: PF3D7_1311800 / Plasmid: pET45b(+) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8IEK1, membrane alanyl aminopeptidase |
---|
-Non-polymers , 6 types, 1676 molecules
#2: Chemical | ChemComp-ZN / | ||||||
---|---|---|---|---|---|---|---|
#3: Chemical | ChemComp-7ML / [( | ||||||
#4: Chemical | #5: Chemical | #6: Chemical | #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: 1.9 Å3/Da / Density % sol: 35.19 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 20% PEG 3350, 0.2M di-sodium malonate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9778 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 7, 2015 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9778 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.33→78.56 Å / Num. obs: 212264 / % possible obs: 99.8 % / Redundancy: 5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.083 / Rpim(I) all: 0.041 / Rrim(I) all: 0.093 / Net I/σ(I): 9.2 / Num. measured all: 1069110 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
|
-Phasing
Phasing | Method: molecular replacement |
---|
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4X2U Resolution: 1.33→49.181 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 21.21
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 69.68 Å2 / Biso mean: 23.335 Å2 / Biso min: 11.98 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.33→49.181 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
|