[English] 日本語
Yorodumi- PDB-6g4p: Non-aged form of Torpedo californica acetylcholinesterase inhibit... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6g4p | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Non-aged form of Torpedo californica acetylcholinesterase inhibited by tabun analog NEDPA bound to uncharged reactivator 2 | |||||||||
Components | Acetylcholinesterase | |||||||||
Keywords | HYDROLASE / acetylcholinesterase / tabun / nerve agent | |||||||||
Function / homology | Function and homology information acetylcholine catabolic process in synaptic cleft / acetylcholinesterase / acetylcholinesterase activity / synaptic cleft / side of membrane / synapse / plasma membrane Similarity search - Function | |||||||||
Biological species | Tetronarce californica (Pacific electric ray) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.83 Å | |||||||||
Authors | Santoni, G. / De la Mora, E. / de Souza, J. / Silman, I. / Sussman, J. / Baati, R. / Weik, M. / Nachon, F. | |||||||||
Funding support | France, 1items
| |||||||||
Citation | Journal: J. Med. Chem. / Year: 2018 Title: Structure-Based Optimization of Nonquaternary Reactivators of Acetylcholinesterase Inhibited by Organophosphorus Nerve Agents. Authors: Santoni, G. / de Sousa, J. / de la Mora, E. / Dias, J. / Jean, L. / Sussman, J.L. / Silman, I. / Renard, P.Y. / Brown, R.C.D. / Weik, M. / Baati, R. / Nachon, F. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6g4p.cif.gz | 443 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6g4p.ent.gz | 362.5 KB | Display | PDB format |
PDBx/mmJSON format | 6g4p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g4/6g4p ftp://data.pdbj.org/pub/pdb/validation_reports/g4/6g4p | HTTPS FTP |
---|
-Related structure data
Related structure data | 6fldC 6fqnC 6g17C 6g4mC 6g4nC 6g4oC 1ea5S S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
-Protein / Sugars , 2 types, 6 molecules AB
#1: Protein | Mass: 60736.516 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) Tetronarce californica (Pacific electric ray) References: UniProt: P04058, acetylcholinesterase #2: Sugar | ChemComp-NAG / |
---|
-Non-polymers , 5 types, 68 molecules
#3: Chemical | #4: Chemical | #5: Chemical | ChemComp-CL / #6: Chemical | #7: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.01 Å3/Da / Density % sol: 59.15 % |
---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.6 / Details: 150mM MES 36% PEG 200 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.03 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 26, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.03 Å / Relative weight: 1 |
Reflection | Resolution: 2.83→45.92 Å / Num. obs: 40548 / % possible obs: 99.2 % / Redundancy: 4.3 % / CC1/2: 0.948 / Net I/σ(I): 3.8 |
Reflection shell | Resolution: 2.72→2.82 Å / Num. unique obs: 3947 / CC1/2: 0.382 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1ea5 Resolution: 2.83→45.92 Å / SU ML: 0.5 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.83→45.92 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|