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- PDB-1p0m: Crystal structure of human butyryl cholinesterase in complex with... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1p0m | |||||||||
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Title | Crystal structure of human butyryl cholinesterase in complex with a choline molecule | |||||||||
![]() | Cholinesterase | |||||||||
![]() | HYDROLASE / serine hydrolase / choline | |||||||||
Function / homology | ![]() cholinesterase / cocaine metabolic process / neuroblast differentiation / Neurotransmitter clearance / cholinesterase activity / choline binding / response to folic acid / response to alkaloid / acetylcholine catabolic process / negative regulation of synaptic transmission ...cholinesterase / cocaine metabolic process / neuroblast differentiation / Neurotransmitter clearance / cholinesterase activity / choline binding / response to folic acid / 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 / Aspirin ADME / nuclear envelope lumen / 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 | ![]() ![]() ![]() | |||||||||
![]() | Nicolet, Y. / Lockridge, O. / Masson, P. / Fontecilla-Camps, J.C. / Nachon, F. | |||||||||
![]() | ![]() Title: Crystal structure of human butyrylcholinesterase and of its complexes with substrate and products. Authors: Nicolet, Y. / Lockridge, O. / Masson, P. / Fontecilla-Camps, J.C. / Nachon, F. #1: ![]() Title: Engineering of a monomeric and low-glycosylated form of human butyrylcholinesterase: expression, purification, characterization and crystallization Authors: Nachon, F. / Nicolet, Y. / Viguie, N. / Masson, P. / Fontecilla-Camps, J.C. / 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 | ![]() | 131.2 KB | Display | ![]() |
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PDB format | ![]() | 100.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 25.9 KB | Display | |
Data in CIF | ![]() | 36.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1p0iSC ![]() 1p0pC ![]() 1p0qC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 59713.512 Da / Num. of mol.: 1 / Mutation: N17Q, N455Q, N481Q, N486Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Sugars , 2 types, 5 molecules ![](data/chem/img/NAG.gif)
#2: Polysaccharide | #3: Sugar | |
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-Non-polymers , 6 types, 272 molecules ![](data/chem/img/SO4.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/MES.gif)
![](data/chem/img/CHT.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/MES.gif)
![](data/chem/img/CHT.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | ChemComp-SO4 / | ||||||||
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#5: Chemical | #6: Chemical | ChemComp-MES / | #7: Chemical | ChemComp-CHT / | #8: Chemical | #9: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.97 Å3/Da / Density % sol: 58.22 % | ||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: Ammonium sulfate, 2-(N-Morpholino)-ethanesulfonic acid, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K | ||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / Method: vapor diffusion, hanging drop / Details: Nachon, F., (2002) Eur.J.Biochem., 269, 630. | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Feb 24, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9798 Å / Relative weight: 1 |
Reflection | Resolution: 2.32→49.43 Å / Num. all: 30739 / Num. obs: 29378 / % possible obs: 87.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1 / Redundancy: 9.9 % / Biso Wilson estimate: 42.7 Å2 / Rsym value: 0.06 / Net I/σ(I): 23.67 |
Reflection shell | Resolution: 2.32→2.47 Å / Redundancy: 6.7 % / Mean I/σ(I) obs: 4.26 / Num. unique all: 4547 / Rsym value: 0.38 / % possible all: 77.7 |
Reflection | *PLUS Rmerge(I) obs: 0.061 |
Reflection shell | *PLUS % possible obs: 77.7 % / Rmerge(I) obs: 0.398 / Mean I/σ(I) obs: 4.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1P0I Resolution: 2.38→49.43 Å / Rfactor Rfree error: 0.006 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber Details: DURING REFINEMENT, THE CATALYTIC S198 WAS MODELLED AS A RESIDUE WITH 2 CONFORMATIONS FOR ITS SIDE CHAIN. ONE OF THESE CORRESPOND TO THE LOCATION OF THE OG IN THE OXANION HOLE. THE ...Details: DURING REFINEMENT, THE CATALYTIC S198 WAS MODELLED AS A RESIDUE WITH 2 CONFORMATIONS FOR ITS SIDE CHAIN. ONE OF THESE CORRESPOND TO THE LOCATION OF THE OG IN THE OXANION HOLE. THE ALTERNATIVE ONE INDCATES THE PRESENCE OF A WATER MOLECULE. DUE TO CONSTRAINTS IN CNS ABOUT MULTIPLE CONFORMATIONS DEFINITION, THE OTHER POSITION FOR THE WATER MOLECULE 205 HAS BEEN ASSIGNED TO A WATER MOLECULE WITH A LOW OCCUPANCY LOCATED IN THE ACYL POCKET
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 100.119 Å2 / ksol: 0.372379 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 49.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.38→49.43 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.38→2.53 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Highest resolution: 2.32 Å | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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