[English] 日本語
Yorodumi- PDB-6tt0: Crystal structure of a potent and reversible dual binding site Ac... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6tt0 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of a potent and reversible dual binding site Acetylcholinesterase chiral inhibitor | ||||||
Components | Acetylcholinesterase | ||||||
Keywords | HYDROLASE / dual binding site inhibitor / chiral separation / acetylcholinesterase / Alzheimer's disease | ||||||
Function / homology | Function and homology information acetylcholine catabolic process in synaptic cleft / acetylcholinesterase / acetylcholinesterase activity / choline metabolic process / side of membrane / synaptic cleft / synapse / extracellular space / plasma membrane Similarity search - Function | ||||||
Biological species | Tetronarce californica (Pacific electric ray) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.80003021833 Å | ||||||
Authors | de la Mora, E. / Mangiatordi, G.F. / Belviso, B.D. / Caliandro, R. / Colletier, J.P. / Catto, M. | ||||||
Citation | Journal: Acs Med.Chem.Lett. / Year: 2020 Title: Chiral Separation, X-ray Structure, and Biological Evaluation of a Potent and Reversible Dual Binding Site AChE Inhibitor. Authors: Catto, M. / Pisani, L. / de la Mora, E. / Belviso, B.D. / Mangiatordi, G.F. / Pinto, A. / Palma, A. / Denora, N. / Caliandro, R. / Colletier, J.P. / Silman, I. / Nicolotti, O. / Altomare, C.D. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6tt0.cif.gz | 135.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6tt0.ent.gz | 94.1 KB | Display | PDB format |
PDBx/mmJSON format | 6tt0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6tt0_validation.pdf.gz | 708.5 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 6tt0_full_validation.pdf.gz | 718.5 KB | Display | |
Data in XML | 6tt0_validation.xml.gz | 22.6 KB | Display | |
Data in CIF | 6tt0_validation.cif.gz | 31.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tt/6tt0 ftp://data.pdbj.org/pub/pdb/validation_reports/tt/6tt0 | HTTPS FTP |
-Related structure data
Related structure data | 2vt7S S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 65315.594 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: T. californica acetylcholinesterase Source: (gene. exp.) Tetronarce californica (Pacific electric ray) Gene: ache Production host: Tetronarce californica (Pacific electric ray) References: UniProt: P04058, acetylcholinesterase | ||||
---|---|---|---|---|---|
#2: Chemical | ChemComp-N9T / ( | ||||
#3: Sugar | #4: 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: 4.1 Å3/Da / Density % sol: 70 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 32% PEG 200 100 mM MES pH 5.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.074 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 28, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.074 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→39.48 Å / Num. obs: 24409 / % possible obs: 98.1 % / Observed criterion σ(I): 1.5 / Redundancy: 1.8 % / Biso Wilson estimate: 67.6781327552 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.04067 / Rpim(I) all: 0.04067 / Rrim(I) all: 0.05751 / Net I/σ(I): 10.5 |
Reflection shell | Resolution: 2.8→2.9 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.3768 / Mean I/σ(I) obs: 1.57 / Num. unique obs: 4385 / CC1/2: 0.872 / Rsym value: 0.5328 / % possible all: 98.81 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2vt7 Resolution: 2.80003021833→39.4797998252 Å / SU ML: 0.395506018796 / Cross valid method: FREE R-VALUE / σ(F): 1.34889918222 / Phase error: 27.3771183945
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 69.9462107358 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.80003021833→39.4797998252 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|