[English] 日本語
Yorodumi- PDB-5ehz: mAChE-syn TZ2PA5 complex from an equimolar mixture of the syn/ant... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5ehz | ||||||
---|---|---|---|---|---|---|---|
Title | mAChE-syn TZ2PA5 complex from an equimolar mixture of the syn/anti isomers | ||||||
Components | Acetylcholinesterase | ||||||
Keywords | HYDROLASE / acetylcholinesterase / inhibitor / click chemistry / triazole | ||||||
Function / homology | Function and homology information acetylcholine metabolic process / serine hydrolase activity / choline binding / acetylcholine catabolic process / acetylcholine binding / acetylcholinesterase / acetylcholine receptor signaling pathway / positive regulation of dendrite morphogenesis / osteoblast development / acetylcholinesterase activity ...acetylcholine metabolic process / serine hydrolase activity / choline binding / acetylcholine catabolic process / acetylcholine binding / acetylcholinesterase / acetylcholine receptor signaling pathway / positive regulation of dendrite morphogenesis / osteoblast development / acetylcholinesterase activity / choline metabolic process / positive regulation of axonogenesis / basement membrane / regulation of receptor recycling / side of membrane / synaptic cleft / laminin binding / synapse assembly / collagen binding / response to insulin / neuromuscular junction / receptor internalization / : / retina development in camera-type eye / presynaptic membrane / nuclear envelope / positive regulation of cold-induced thermogenesis / postsynaptic membrane / cell adhesion / endoplasmic reticulum lumen / axon / neuronal cell body / synapse / dendrite / perinuclear region of cytoplasm / Golgi apparatus / cell surface / protein homodimerization activity / extracellular space / identical protein binding / plasma membrane Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Bourne, Y. / Marchot, P. | ||||||
Citation | Journal: J.Am.Chem.Soc. / Year: 2016 Title: Steric and Dynamic Parameters Influencing In Situ Cycloadditions to Form Triazole Inhibitors with Crystalline Acetylcholinesterase. Authors: Bourne, Y. / Sharpless, K.B. / Taylor, P. / Marchot, P. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5ehz.cif.gz | 435.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5ehz.ent.gz | 358.6 KB | Display | PDB format |
PDBx/mmJSON format | 5ehz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5ehz_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 5ehz_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 5ehz_validation.xml.gz | 24.1 KB | Display | |
Data in CIF | 5ehz_validation.cif.gz | 37.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/eh/5ehz ftp://data.pdbj.org/pub/pdb/validation_reports/eh/5ehz | HTTPS FTP |
-Related structure data
Related structure data | 5ehnC 5ehqC 5eiaC 5eieC 5eihC 1j06S C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 59764.488 Da / Num. of mol.: 2 / Fragment: UNP residues 32-574 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ache / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: P21836, acetylcholinesterase #2: Sugar | #3: Chemical | #4: Chemical | ChemComp-P6G / | #5: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
---|
-Sample preparation
Crystal | Density Matthews: 4.17 Å3/Da / Density % sol: 70.5 % |
---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop Details: 25-35% PEG550 MME or PEG600, 60-100 mM Hepes or sodium acetate PH range: 6.5-8.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.931 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 13, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.931 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→44 Å / Num. obs: 69707 / % possible obs: 99.7 % / Redundancy: 4.9 % / Biso Wilson estimate: 57.21 Å2 / Rsym value: 0.072 / Net I/σ(I): 21.6 |
Reflection shell | Resolution: 2.5→2.64 Å / Redundancy: 5 % / Rmerge(I) obs: 0.688 / Mean I/σ(I) obs: 3.1 / % possible all: 99.7 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1J06 Resolution: 2.5→44 Å / Cor.coef. Fo:Fc: 0.9248 / Cor.coef. Fo:Fc free: 0.9142 / SU R Cruickshank DPI: 0.225 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.226 / SU Rfree Blow DPI: 0.174 / SU Rfree Cruickshank DPI: 0.176
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 53.38 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.298 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.5→44 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.5→2.56 Å / Total num. of bins used: 20
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|