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Open data
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Basic information
Entry | Database: PDB / ID: 2xmg | |||||||||
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Title | G117H mutant of human butyrylcholinesterase in complex with VX | |||||||||
![]() | CHOLINESTERASE | |||||||||
![]() | HYDROLASE / GLYCOPROTEIN | |||||||||
Function / homology | ![]() cholinesterase / cocaine metabolic process / neuroblast differentiation / Neurotransmitter clearance / cholinesterase activity / response to folic acid / choline binding / response to alkaloid / acetylcholine catabolic process / negative regulation of synaptic transmission ...cholinesterase / cocaine metabolic process / neuroblast differentiation / Neurotransmitter clearance / cholinesterase activity / response to folic acid / choline binding / response to alkaloid / acetylcholine catabolic process / negative regulation of synaptic transmission / peptide hormone processing / acetylcholinesterase activity / choline metabolic process / hydrolase activity, acting on ester bonds / nuclear envelope lumen / Aspirin ADME / Synthesis of PC / Synthesis, secretion, and deacylation of Ghrelin / catalytic activity / response to glucocorticoid / xenobiotic metabolic process / learning / amyloid-beta binding / blood microparticle / negative regulation of cell population proliferation / endoplasmic reticulum lumen / enzyme binding / extracellular space / extracellular region / identical protein binding / plasma membrane Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Nachon, F. / Carletti, E. / Wandhammer, M. / Nicolet, Y. / Schopfer, L.M. / Masson, P. / Lockridge, O. | |||||||||
![]() | ![]() Title: X-Ray Crystallographic Snapshots of Reaction Intermediates in the G117H Mutant of Human Butyrylcholinesterase, a Nerve Agent Target Engineered Into a Catalytic Bioscavenge Authors: Nachon, F. / Carletti, E. / Wandhammer, M. / Nicolet, Y. / Schopfer, L.M. / Masson, P. / Lockridge, O. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 236.2 KB | Display | ![]() |
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PDB format | ![]() | 190.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.3 MB | Display | ![]() |
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Full document | ![]() | 1.3 MB | Display | |
Data in XML | ![]() | 24.5 KB | Display | |
Data in CIF | ![]() | 34.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2xmbC ![]() 2xmcC ![]() 2xmdC ![]() 1p0iS 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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Unit cell |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 59794.605 Da / Num. of mol.: 1 / Fragment: RESIDUES 29-557 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Sugars , 3 types, 6 molecules ![](data/chem/img/NAG.gif)
#2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: Polysaccharide | beta-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #9: Sugar | |
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-Non-polymers , 6 types, 167 molecules ![](data/chem/img/UNX.gif)
![](data/chem/img/VX.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/NH4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/VX.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/NH4.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | ChemComp-UNX / #5: Chemical | ChemComp-VX / | #6: Chemical | ChemComp-SO4 / | #7: Chemical | ChemComp-CL / #8: Chemical | #10: Water | ChemComp-HOH / | |
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-Details
Compound details | ENGINEERED RESIDUE IN CHAIN A, ASN 45 TO GLN ENGINEERED RESIDUE IN CHAIN A, GLY 145 TO HIS ...ENGINEERED |
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Sequence details | FIVE MUTATIONS, N17Q, G117H, N455Q, N481Q, N486Q |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.8 Å3/Da / Density % sol: 56 % / Description: NONE |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6 Details: AMMONIUM SULFATE 2.1 M, 2-(N-MORPHOLINO)-ETHANESULFONIC ACID 0.1 M, PH 6.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Nov 6, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8726 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→110 Å / Num. obs: 20940 / % possible obs: 94.3 % / Observed criterion σ(I): -3 / Redundancy: 8 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 23.7 |
Reflection shell | Resolution: 2.7→2.8 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 3.8 / % possible all: 95 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1P0I Resolution: 2.7→110.43 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.907 / SU B: 25.354 / SU ML: 0.239 / Cross valid method: THROUGHOUT / ESU R: 0.765 / ESU R Free: 0.333 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 56.147 Å2
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Refinement step | Cycle: LAST / Resolution: 2.7→110.43 Å
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