+Open data
-Basic information
Entry | Database: PDB / ID: 6eqq | |||||||||
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Title | Human butyrylcholinesterase in complex with huprine 19 | |||||||||
Components | Cholinesterase | |||||||||
Keywords | HYDROLASE / Complex / Inhibitor / huprine | |||||||||
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: 2.40000447819 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 | 6eqq.cif.gz | 281 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6eqq.ent.gz | 189.3 KB | Display | PDB format |
PDBx/mmJSON format | 6eqq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/eq/6eqq ftp://data.pdbj.org/pub/pdb/validation_reports/eq/6eqq | HTTPS FTP |
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-Related structure data
Related structure data | 6ep4C 6eqpC 6esjC 6esyC 1p0iS 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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Unit cell |
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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.) 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 , 3 types, 6 molecules
#2: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
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#3: Polysaccharide | beta-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
#5: Sugar | ChemComp-NAG / |
-Non-polymers , 7 types, 223 molecules
#4: Chemical | ChemComp-H19 / | ||||||||
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#6: Chemical | ChemComp-BR / | ||||||||
#7: Chemical | ChemComp-CL / #8: Chemical | #9: Chemical | ChemComp-GOL / #10: Chemical | ChemComp-UNL / | Mass: 90.121 Da / Num. of mol.: 1 / Source method: obtained synthetically #11: 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: 63.42 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 0.1 M 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: ID29 / Wavelength: 0.979 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 31, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→57.13 Å / Num. obs: 31862 / % possible obs: 99.91 % / Redundancy: 9.5 % / Biso Wilson estimate: 46.4867618287 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.09373 / Rpim(I) all: 0.03181 / Rrim(I) all: 0.0991 / Net I/σ(I): 17.14 |
Reflection shell | Resolution: 2.4→2.486 Å / Redundancy: 9.1 % / Rmerge(I) obs: 0.922 / Mean I/σ(I) obs: 2.21 / Num. unique obs: 3154 / CC1/2: 0.807 / Rpim(I) all: 0.3206 / Rrim(I) all: 0.9772 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1P0I Resolution: 2.40000447819→57.1280859052 Å / SU ML: 0.218521836804 / Cross valid method: FREE R-VALUE / σ(F): 1.34365534751 / Phase error: 21.4809239337
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 60.3772836568 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.40000447819→57.1280859052 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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