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Yorodumi- PDB-7zpb: Structure of hemiacetylated human butyrylcholinesterase upon reac... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7zpb | ||||||
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Title | Structure of hemiacetylated human butyrylcholinesterase upon reaction with 8-(3-(4-(prop-2-yn-1-yl)piperazin-1-yl)propoxy)quinoline-2-carbaldehyde | ||||||
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 / 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: 2.31 Å | ||||||
Authors | Denic, M. / Chioua, M. / Knez, D. / Gobec, S. / Nachon, F. / Marco-Contelles, J.L. / Brazzolotto, X. | ||||||
Funding support | France, 1items
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Citation | Journal: Acta Pharm Sin B / Year: 2023 Title: 8-Hydroxyquinolylnitrones as multifunctional ligands for the therapy of neurodegenerative diseases. Authors: Knez, D. / Diez-Iriepa, D. / Chioua, M. / Gottinger, A. / Denic, M. / Chantegreil, F. / Nachon, F. / Brazzolotto, X. / Skrzypczak-Wiercioch, A. / Meden, A. / Pislar, A. / Kos, J. / Zakelj, S. ...Authors: Knez, D. / Diez-Iriepa, D. / Chioua, M. / Gottinger, A. / Denic, M. / Chantegreil, F. / Nachon, F. / Brazzolotto, X. / Skrzypczak-Wiercioch, A. / Meden, A. / Pislar, A. / Kos, J. / Zakelj, S. / Stojan, J. / Salat, K. / Serrano, J. / Fernandez, A.P. / Sanchez-Garcia, A. / Martinez-Murillo, R. / Binda, C. / Lopez-Munoz, F. / Gobec, S. / Marco-Contelles, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7zpb.cif.gz | 278.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7zpb.ent.gz | 187.2 KB | Display | PDB format |
PDBx/mmJSON format | 7zpb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zp/7zpb ftp://data.pdbj.org/pub/pdb/validation_reports/zp/7zpb | HTTPS FTP |
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-Related structure data
Related structure data | 7qbqC 7qbrC 7zw3C 6qaaS 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 mutations compared to mature wild type sequence to avoid too much N-glycozylation. Numeration on the maturated enzyme (devoid of the signal peptide) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: BCHE, CHE1 / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P06276, cholinesterase |
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-Sugars , 4 types, 7 molecules
#2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: Polysaccharide | Source method: isolated from a genetically manipulated source #4: Sugar | ChemComp-NAG / | #7: Sugar | ChemComp-SIA / | |
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-Non-polymers , 6 types, 123 molecules
#5: Chemical | #6: Chemical | ChemComp-JS0 / [ | #8: Chemical | ChemComp-MES / | #9: Chemical | ChemComp-PPI / | #10: Chemical | ChemComp-SO4 / #11: Water | ChemComp-HOH / | |
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-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: 3.19 Å3/Da / Density % sol: 61.44 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: Ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.976253 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 3, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976253 Å / Relative weight: 1 |
Reflection | Resolution: 2.31→109.1 Å / Num. obs: 34171 / % possible obs: 99.76 % / Redundancy: 8.6 % / Biso Wilson estimate: 49.62 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.07855 / Rpim(I) all: 0.02818 / Rrim(I) all: 0.0837 / Net I/σ(I): 15.78 |
Reflection shell | Resolution: 2.31→2.393 Å / Redundancy: 8.9 % / Rmerge(I) obs: 0.8594 / Mean I/σ(I) obs: 2.37 / Num. unique obs: 3358 / CC1/2: 0.752 / Rpim(I) all: 0.3066 / Rrim(I) all: 0.9146 / % possible all: 99.94 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6QAA Resolution: 2.31→109.07 Å / SU ML: 0.2492 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.127 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 58.16 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.31→109.07 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: 16.641344389 Å / Origin y: 32.0111963813 Å / Origin z: 39.07867261 Å
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Refinement TLS group | Selection details: (chain 'A' and resid 4 through 529) |