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Yorodumi- PDB-8am2: Human butyrylcholinesterase in complex with 2,2'-(((1E,1'E)-(2-ph... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8am2 | ||||||
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Title | Human butyrylcholinesterase in complex with 2,2'-(((1E,1'E)-(2-phenylpyrimidine-4,6-diyl)bis(methaneylylidene))bis(hydrazin-1-yl-2-ylidene))bis(N,N,N-trimethyl-2-oxoethan-1-aminium) | ||||||
Components | Cholinesterase | ||||||
Keywords | HYDROLASE / Inhibitor / complex / butyrylcholinesterase | ||||||
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: 2.5 Å | ||||||
Authors | Nachon, F. / Brazzolotto, X. / Dias, J. | ||||||
Funding support | France, 1items
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Citation | Journal: Chembiochem / Year: 2022 Title: Grid-Type Quaternary Metallosupramolecular Compounds Inhibit Human Cholinesterases through Dynamic Multivalent Interactions. Authors: Nachon, F. / Brazzolotto, X. / Dias, J. / Courageux, C. / Drozdz, W. / Cao, X.Y. / Stefankiewicz, A.R. / Lehn, J.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8am2.cif.gz | 279.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8am2.ent.gz | 189.6 KB | Display | PDB format |
PDBx/mmJSON format | 8am2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8am2_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 8am2_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 8am2_validation.xml.gz | 24.1 KB | Display | |
Data in CIF | 8am2_validation.cif.gz | 33.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/am/8am2 ftp://data.pdbj.org/pub/pdb/validation_reports/am/8am2 | HTTPS FTP |
-Related structure data
Related structure data | 8aenC 8aevC 8am1C 1p0iS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-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 Details: engineered butyrylcholinesterase for crystallisation Source: (gene. exp.) Homo sapiens (human) / Gene: BCHE, CHE1 / 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 , 5 types, 190 molecules
#3: Chemical | ChemComp-N0C / ~{ | ||||
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#5: Chemical | ChemComp-GOL / | ||||
#6: Chemical | ChemComp-SO4 / #7: Chemical | #8: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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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: 3.22 Å3/Da / Density % sol: 61.75 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: AMMONIUM SULFATE 2.1 M, 2-(N-MORPHOLINO)-ETHANESULFONIC ACID 0.1 M |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.07252 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 24, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.07252 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→55.25 Å / Num. obs: 26526 / % possible obs: 97.46 % / Redundancy: 6.4 % / Biso Wilson estimate: 46.82 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.05889 / Rpim(I) all: 0.02449 / Rrim(I) all: 0.06401 / Net I/σ(I): 25.04 |
Reflection shell | Resolution: 2.5→2.589 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.4761 / Mean I/σ(I) obs: 3.56 / Num. unique obs: 2653 / CC1/2: 0.89 / CC star: 0.971 / Rpim(I) all: 0.1955 / Rrim(I) all: 0.5164 / % possible all: 98.77 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1P0I Resolution: 2.5→55.25 Å / SU ML: 0.2806 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.5561 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: 53.41 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→55.25 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 | Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A
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