+Open data
-Basic information
Entry | Database: PDB / ID: 6esj | |||||||||
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Title | Human butyrylcholinesterase in complex with propidium | |||||||||
Components | Cholinesterase | |||||||||
Keywords | HYDROLASE / Butyrylcholinesterase / Inhibitor / Complex | |||||||||
Function / homology | Function and homology information cholinesterase / cocaine metabolic process / neuroblast differentiation / Neurotransmitter clearance / choline metabolic process / 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 / choline metabolic process / choline binding / response to folic acid / response to alkaloid / acetylcholine catabolic process / negative regulation of synaptic transmission / cholinesterase activity / peptide hormone processing / acetylcholinesterase activity / 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 / endoplasmic reticulum lumen / negative regulation of cell population proliferation / 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: 2.97984513804 Å | |||||||||
Authors | Nachon, F. / Brazzolotto, X. / Wandhammer, M. / Trovaslet-Leroy, M. / Macdonald, I.R. / Darvesh, S. / Rosenberry, T.L. | |||||||||
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 | 6esj.cif.gz | 535.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6esj.ent.gz | 373.8 KB | Display | PDB format |
PDBx/mmJSON format | 6esj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/es/6esj ftp://data.pdbj.org/pub/pdb/validation_reports/es/6esj | HTTPS FTP |
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-Related structure data
Related structure data | 6ep4C 6eqpC 6eqqC 6esyC 5dywS 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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2 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 59657.402 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: BCHE, CHE1 / Cell line (production host): S2 / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: P06276, cholinesterase |
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-Sugars , 2 types, 12 molecules
#2: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source #3: Sugar | ChemComp-NAG / |
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-Non-polymers , 4 types, 148 molecules
#4: Chemical | #5: Chemical | ChemComp-CL / #6: Chemical | ChemComp-GLY / | #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.86 Å3/Da / Density % sol: 56.98 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4 Details: 0.2 M Ammonium Sulfate, 12% Polyethylene glycol 4000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 1.00442 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 2, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.00442 Å / Relative weight: 1 |
Reflection | Resolution: 2.979→38.06 Å / Num. obs: 27721 / % possible obs: 96.74 % / Redundancy: 3.5 % / Biso Wilson estimate: 72.6781451165 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.09197 / Rpim(I) all: 0.05716 / Rrim(I) all: 0.1087 / Net I/σ(I): 10.83 |
Reflection shell | Resolution: 2.979→3.087 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.567 / Mean I/σ(I) obs: 2.01 / Num. unique obs: 2638 / CC1/2: 0.728 / Rpim(I) all: 0.3415 / Rrim(I) all: 0.6604 / % possible all: 93.55 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5dyw Resolution: 2.97984513804→38.0583333333 Å / SU ML: 0.490852176003 / Cross valid method: FREE R-VALUE / σ(F): 1.36869738513 / Phase error: 31.9085285236
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 81.2509924017 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.97984513804→38.0583333333 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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