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- PDB-2whp: Crystal structure of acetylcholinesterase, phosphonylated by sari... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2whp | ||||||
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Title | Crystal structure of acetylcholinesterase, phosphonylated by sarin and in complex with HI-6 | ||||||
![]() | (ACETYLCHOLINESTERASE) x 2 | ||||||
![]() | HYDROLASE / SERINE ESTERASE / ALTERNATIVE SPLICING / NEUROTRANSMITTER DEGRADATION / HI-6 / SARIN / SYNAPSE / MEMBRANE / SECRETED / CELL MEMBRANE / DISULFIDE BOND / CHOLINESTERASE / GPI-ANCHOR / LIPOPROTEIN / GLYCOPROTEIN / CELL JUNCTION | ||||||
Function / homology | ![]() acetylcholine metabolic process / serine hydrolase activity / choline binding / acetylcholine catabolic process / acetylcholine binding / acetylcholinesterase / acetylcholine receptor signaling pathway / positive regulation of dendrite morphogenesis / osteoblast development / acetylcholinesterase activity ...acetylcholine metabolic process / serine hydrolase activity / choline binding / acetylcholine catabolic process / acetylcholine binding / acetylcholinesterase / acetylcholine receptor signaling pathway / positive regulation of dendrite morphogenesis / osteoblast development / acetylcholinesterase activity / choline metabolic process / positive regulation of axonogenesis / basement membrane / regulation of receptor recycling / side of membrane / synaptic cleft / laminin binding / synapse assembly / collagen binding / response to insulin / neuromuscular junction / receptor internalization / : / retina development in camera-type eye / nuclear envelope / presynaptic membrane / positive regulation of cold-induced thermogenesis / postsynaptic membrane / cell adhesion / endoplasmic reticulum lumen / axon / neuronal cell body / synapse / dendrite / perinuclear region of cytoplasm / Golgi apparatus / cell surface / protein homodimerization activity / extracellular space / identical protein binding / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Ekstrom, F. / Hornberg, A. / Artursson, E. / Hammarstrom, L.G. / Schneider, G. / Pang, Y.P. | ||||||
![]() | ![]() Title: Structure of Hi-6Sarin-Acetylcholinesterase Determined by X-Ray Crystallography and Molecular Dynamics Simulation: Reactivator Mechanism and Design. Authors: Ekstrom, F. / Hornberg, A. / Artursson, E. / Hammarstrom, L.G. / Schneider, G. / Pang, Y.P. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 459.5 KB | Display | ![]() |
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PDB format | ![]() | 376.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.2 MB | Display | ![]() |
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Full document | ![]() | 1.3 MB | Display | |
Data in XML | ![]() | 49.4 KB | Display | |
Data in CIF | ![]() | 71.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2whqC ![]() 2whrC ![]() 1j06S C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 60354.070 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN, RESIDUES 32-573 Source method: isolated from a genetically manipulated source Details: CATALYTIC SER203 PHOSPHONYLATED BY SARIN / Source: (gene. exp.) ![]() ![]() Cell line (production host): HUMAN EMBRYONIC KIDNEY (HEK) 293 CELLS Production host: ![]() |
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#2: Protein | Mass: 60341.031 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN, RESIDUES 32-573 Source method: isolated from a genetically manipulated source Details: CATALYTIC SER203 PHOSPHONYLATED BY SARIN / Source: (gene. exp.) ![]() ![]() Cell line (production host): HUMAN EMBRYONIC KIDNEY (HEK) 293 CELLS Production host: ![]() |
-Sugars , 1 types, 3 molecules ![](data/chem/img/NAG.gif)
#3: Sugar |
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-Non-polymers , 5 types, 798 molecules ![](data/chem/img/HI6.gif)
![](data/chem/img/CO3.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/P6G.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CO3.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/P6G.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | #5: Chemical | ChemComp-CO3 / | #6: Chemical | ChemComp-PEG / | #7: Chemical | ChemComp-P6G / | #8: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.1 Å3/Da / Density % sol: 70 % / Description: NONE |
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Crystal grow | pH: 7 / Details: 26-30 % (V/V) PEG750MME 0.1 M HEPES PH 7.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Feb 21, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.041 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→29.8 Å / Num. obs: 102346 / % possible obs: 99.2 % / Observed criterion σ(I): 3 / Redundancy: 7.5 % / Biso Wilson estimate: 38.88 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 21.9 |
Reflection shell | Resolution: 2.2→2.32 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 5.1 / % possible all: 98.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1J06 Resolution: 2.2→28.988 Å / SU ML: 0.3 / σ(F): 1.36 / Phase error: 20.21 / Stereochemistry target values: ML / Details: RESIDUES 258-264 ARE DISORDERED
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 71.363 Å2 / ksol: 0.353 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.2→28.988 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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