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Yorodumi- PDB-3zlv: Crystal structure of mouse acetylcholinesterase in complex with t... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3zlv | ||||||
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Title | Crystal structure of mouse acetylcholinesterase in complex with tabun and HI-6 | ||||||
Components | ACETYLCHOLINESTERASE | ||||||
Keywords | HYDROLASE / RVX / RUSSIAN VX / CYCLOSARIN | ||||||
Function / homology | Function and homology information acetylcholine metabolic process / serine hydrolase activity / choline metabolic process / choline binding / acetylcholine catabolic process / acetylcholine binding / acetylcholinesterase / cholinesterase activity / acetylcholine receptor signaling pathway / positive regulation of dendrite morphogenesis ...acetylcholine metabolic process / serine hydrolase activity / choline metabolic process / choline binding / acetylcholine catabolic process / acetylcholine binding / acetylcholinesterase / cholinesterase activity / acetylcholine receptor signaling pathway / positive regulation of dendrite morphogenesis / osteoblast development / acetylcholinesterase activity / positive regulation of axonogenesis / basement membrane / regulation of receptor recycling / synaptic cleft / laminin binding / side of membrane / synapse assembly / collagen binding / neuromuscular junction / response to insulin / receptor internalization / : / retina development in camera-type eye / presynaptic membrane / nuclear envelope / positive regulation of cold-induced thermogenesis / postsynaptic membrane / hydrolase activity / cell adhesion / axon / endoplasmic reticulum lumen / dendrite / neuronal cell body / synapse / perinuclear region of cytoplasm / Golgi apparatus / cell surface / protein homodimerization activity / extracellular space / extracellular region / membrane / identical protein binding / plasma membrane Similarity search - Function | ||||||
Biological species | MUS MUSCULUS (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Artursson, E. / Andersson, P.O. / Akfur, C. / Linusson, A. / Borjegren, S. / Ekstrom, F. | ||||||
Citation | Journal: Biochem.Pharmacol. / Year: 2013 Title: Catalytic-Site Conformational Equilibrium in Nerve-Agent Adducts of Acetylcholinesterase; Possible Implications for the Hi-6 Antidote Substrate Specificity. Authors: Artursson, E. / Andersson, P.O. / Akfur, C. / Linusson, A. / Borjegren, S. / Ekstrom, F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3zlv.cif.gz | 237.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3zlv.ent.gz | 189.8 KB | Display | PDB format |
PDBx/mmJSON format | 3zlv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zl/3zlv ftp://data.pdbj.org/pub/pdb/validation_reports/zl/3zlv | HTTPS FTP |
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-Related structure data
Related structure data | 3zltC 3zluC 1j06S C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given / Matrix: (1), |
-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 59899.590 Da / Num. of mol.: 2 / Fragment: CATALYTIC DOMAIN, RESIDUES 32-574 Source method: isolated from a genetically manipulated source Details: CATALYTIC SER203 PHOSPHOAMIDATED BY TABUN / Source: (gene. exp.) MUS MUSCULUS (house mouse) / Cell line (production host): HEK293F / Production host: HOMO SAPIENS (human) / References: UniProt: P21836, acetylcholinesterase |
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-Non-polymers , 5 types, 685 molecules
#2: Chemical | #3: Chemical | ChemComp-CO3 / | #4: Chemical | ChemComp-1KA / ( #5: Chemical | ChemComp-PE4 / | #6: Water | ChemComp-HOH / | |
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-Details
Sequence details | C-TERMINAL EXPRESSION |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.24 Å3/Da / Density % sol: 70.96 % / Description: NONE |
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Crystal grow | pH: 7 / Details: pH 7 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: MAX II / Beamline: I911-3 / Wavelength: 1.04123 |
Detector | Type: MARREASERCH / Detector: CCD / Date: Jun 26, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.04123 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→29.21 Å / Num. obs: 71276 / % possible obs: 99.9 % / Observed criterion σ(I): 3 / Redundancy: 7.4 % / Biso Wilson estimate: 48.97 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 17 |
Reflection shell | Resolution: 2.5→2.64 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 4.9 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1J06 Resolution: 2.5→29.193 Å / SU ML: 0.38 / σ(F): 1.39 / Phase error: 21.21 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 64.75 Å2 / ksol: 0.342 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.5→29.193 Å
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Refine LS restraints |
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LS refinement shell |
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