+Open data
-Basic information
Entry | Database: PDB / ID: 6ep4 | |||||||||
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Title | Human butyrylcholinesterase in complex with decamethonium | |||||||||
Components | Cholinesterase | |||||||||
Keywords | HYDROLASE / Complex / Inhibitor / Quaternary Ammonium | |||||||||
Function / homology | Function and homology information 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 | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.30005381157 Å | |||||||||
Authors | Nachon, F. / Brazzolotto, X. / Wandhammer, M. / Trovaslet-Leroy, M. / Rosenberry, T.L. / Macdonald, I.R. / Darvesh, S. | |||||||||
Funding support | France, 1items
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Citation | Journal: Molecules / Year: 2017 Title: Comparison of the Binding of Reversible Inhibitors to Human Butyrylcholinesterase and Acetylcholinesterase: A Crystallographic, Kinetic and Calorimetric Study. Authors: Rosenberry, T.L. / Brazzolotto, X. / Macdonald, I.R. / Wandhammer, M. / Trovaslet-Leroy, M. / Darvesh, S. / Nachon, F. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ep4.cif.gz | 281.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ep4.ent.gz | 190.3 KB | Display | PDB format |
PDBx/mmJSON format | 6ep4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ep/6ep4 ftp://data.pdbj.org/pub/pdb/validation_reports/ep/6ep4 | HTTPS FTP |
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-Related structure data
Related structure data | 6eqpC 6eqqC 6esjC 6esyC 1p0iS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-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: 59713.512 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: BCHE, CHE1 / Plasmid: pGS / Cell line (production host): CHO-K1 / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P06276, cholinesterase |
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-Sugars , 2 types, 6 molecules
#2: Polysaccharide | Source method: isolated from a genetically manipulated source #4: Sugar | ChemComp-NAG / |
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-Non-polymers , 4 types, 250 molecules
#3: Chemical | ChemComp-DME / | ||
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#5: Chemical | ChemComp-SO4 / | ||
#6: Chemical | #7: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.36 Å3/Da / Density % sol: 63.39 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 0.1 MES Buffer, 2.1 M ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.934 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 25, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→42.4 Å / Num. obs: 35717 / % possible obs: 99.3 % / Redundancy: 9.1 % / Biso Wilson estimate: 41.2382916228 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.05305 / Rpim(I) all: 0.01813 / Rrim(I) all: 0.05618 / Net I/σ(I): 29.63 |
Reflection shell | Resolution: 2.3→2.382 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.3782 / Mean I/σ(I) obs: 4.82 / Num. unique obs: 3390 / CC1/2: 0.939 / Rpim(I) all: 0.0694 / Rrim(I) all: 0.4171 / % possible all: 95.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1P0I Resolution: 2.30005381157→42.3929730068 Å / SU ML: 0.268497481387 / Cross valid method: FREE R-VALUE / σ(F): 1.3561261554 / Phase error: 22.0103736751 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 49.960587464 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.30005381157→42.3929730068 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -16.1381013377 Å / Origin y: -32.6231509677 Å / Origin z: -26.7350254707 Å
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Refinement TLS group | Selection details: chain A |