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Yorodumi- PDB-4bdt: Human acetylcholinesterase in complex with huprine W and fasciculin 2 -
+Open data
-Basic information
Entry | Database: PDB / ID: 4bdt | |||||||||
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Title | Human acetylcholinesterase in complex with huprine W and fasciculin 2 | |||||||||
Components |
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Keywords | HYDROLASE/INHIBITOR / HYDROLASE-INHIBITOR COMPLEX / BUTYRYLCHOLINESTERASE / NERVE TRANSMISSION / INHIBITION / ALPHA-BETA HYDROLASE | |||||||||
Function / homology | Function and homology information negative regulation of synaptic transmission, cholinergic / Neurotransmitter clearance / acetylcholine catabolic process in synaptic cleft / cholinesterase activity / serine hydrolase activity / acetylcholine catabolic process / acetylcholine binding / acetylcholinesterase / amyloid precursor protein metabolic process / acetylcholine receptor signaling pathway ...negative regulation of synaptic transmission, cholinergic / Neurotransmitter clearance / acetylcholine catabolic process in synaptic cleft / cholinesterase activity / serine hydrolase activity / acetylcholine catabolic process / acetylcholine binding / acetylcholinesterase / amyloid precursor protein metabolic process / acetylcholine receptor signaling pathway / osteoblast development / acetylcholinesterase activity / Synthesis of PC / basement membrane / Synthesis, secretion, and deacylation of Ghrelin / regulation of receptor recycling / synaptic cleft / side of membrane / laminin binding / collagen binding / synapse assembly / positive regulation of protein secretion / neuromuscular junction / receptor internalization / positive regulation of cold-induced thermogenesis / retina development in camera-type eye / nervous system development / amyloid-beta binding / toxin activity / cell adhesion / hydrolase activity / synapse / perinuclear region of cytoplasm / Golgi apparatus / cell surface / protein homodimerization activity / extracellular space / extracellular region / membrane / nucleus / plasma membrane Similarity search - Function | |||||||||
Biological species | HOMO SAPIENS (human) DENDROASPIS ANGUSTICEPS (eastern green mamba) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.104 Å | |||||||||
Authors | Nachon, F. / Carletti, E. / Ronco, C. / Trovaslet, M. / Nicolet, Y. / Jean, L. / Renard, P.-Y. | |||||||||
Citation | Journal: Biochem. J. / Year: 2013 Title: Crystal structures of human cholinesterases in complex with huprine W and tacrine: elements of specificity for anti-Alzheimer's drugs targeting acetyl- and butyryl-cholinesterase. Authors: Nachon, F. / Carletti, E. / Ronco, C. / Trovaslet, M. / Nicolet, Y. / Jean, L. / Renard, P.Y. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4bdt.cif.gz | 265.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4bdt.ent.gz | 213.4 KB | Display | PDB format |
PDBx/mmJSON format | 4bdt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4bdt_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 4bdt_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 4bdt_validation.xml.gz | 26.2 KB | Display | |
Data in CIF | 4bdt_validation.cif.gz | 36.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bd/4bdt ftp://data.pdbj.org/pub/pdb/validation_reports/bd/4bdt | HTTPS FTP |
-Related structure data
Related structure data | 4bdsC 2x8bS 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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2 |
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3 |
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Unit cell |
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Components on special symmetry positions |
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Details | CHAINA FORMS A BIOLOGICAL DIMER WITH A SYMMETRIC MOLECULE BY INTERACTION OF 4 HELICES. THE DODECAMETRIC ASSEMBLY SHOWN IN THE ASSEMBLY INFORMATION RESULTS FROM THE ASSOCIATION OF 3 BIOLOGICAL DIMERS. |
-Components
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 64641.738 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PGS / Cell line (production host): CHO-K1 / Production host: CRICETULUS GRISEUS (Chinese hamster) / References: UniProt: P22303, acetylcholinesterase |
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#2: Protein | Mass: 6768.769 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) DENDROASPIS ANGUSTICEPS (eastern green mamba) References: UniProt: P0C1Z0 |
-Sugars , 1 types, 1 molecules
#3: 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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-Non-polymers , 4 types, 131 molecules
#4: Chemical | ChemComp-HUW / | ||||
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#5: Chemical | ChemComp-CL / #6: Chemical | ChemComp-SO4 / | #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: 4.9 Å3/Da / Density % sol: 75 % / Description: NONE |
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Crystal grow | pH: 7.4 / Details: 0.1 M HEPES BUFFER PH 7.4, 1.3 M AMMONIUM SULFATE |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.979 |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 19, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 3.1→58 Å / Num. obs: 19677 / % possible obs: 98.1 % / Observed criterion σ(I): -3 / Redundancy: 3.1 % / Biso Wilson estimate: 66.43 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 16 |
Reflection shell | Resolution: 3.1→3.2 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.66 / Mean I/σ(I) obs: 3 / % possible all: 93.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2X8B Resolution: 3.104→57.934 Å / SU ML: 0.36 / σ(F): 1.35 / Phase error: 26.12 / Stereochemistry target values: ML
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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: 48.2 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.104→57.934 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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