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- PDB-5brx: X-ray crystal structure of Aplysia californica (Ac-AChBP) in comp... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5brx | ||||||
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Title | X-ray crystal structure of Aplysia californica (Ac-AChBP) in complex with 2-pyridyl azatricyclo[3.3.1.13,7]decane; 2-pyridylazaadamantane; 2-Aza (TI-8480) | ||||||
![]() | Soluble acetylcholine receptor | ||||||
![]() | ACETYLCHOLINE BINDING PROTEIN / AChBP / nicotine / acetylcholine | ||||||
Function / homology | ![]() acetylcholine receptor activity / acetylcholine-gated monoatomic cation-selective channel activity / response to nicotine / neuron projection / synapse / identical protein binding / membrane / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Bobango, J. / Sankaran, B. / Park, J.F. / Wu, J. / Talley, T.T. | ||||||
![]() | ![]() Title: Comparisons of Binding Affinities for Neuronal Nicotinic Receptors (NNRs) and AChBPs Authors: Bobango, J. / Sankaran, B. / Park, J.F. / Wu, J. / Talley, T.T. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 429.8 KB | Display | ![]() |
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PDB format | ![]() | 348.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 531.1 KB | Display | ![]() |
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Full document | ![]() | 541 KB | Display | |
Data in XML | ![]() | 74.5 KB | Display | |
Data in CIF | ![]() | 101.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5bp0C ![]() 5bw2C ![]() 2bynS ![]() 2byrS ![]() 2bysS ![]() 2pgzS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 26235.141 Da / Num. of mol.: 10 / Fragment: UNP residues 18-236 / Mutation: Y55W Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Cell line (production host): HEK GNT1- / Production host: ![]() #2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-TI4 / ( #4: Chemical | ChemComp-PG4 / #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.49 Å3/Da / Density % sol: 50.57 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 1.7% PEG 400, 0.085 M HEPES - Na pH 7.5, 1.7 M Ammonium Sulfate, 15% Glycerol |
-Data collection
Diffraction | Mean temperature: 88 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 10, 2010 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.05→50 Å / Num. obs: 159523 / % possible obs: 100 % / Redundancy: 12.7 % / Biso Wilson estimate: 22.9 Å2 / Rmerge(I) obs: 0.156 / Χ2: 1.072 / Net I/av σ(I): 17.273 / Net I/σ(I): 5.5 / Num. measured all: 2019957 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _ / % possible all: 100
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Processing
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Refinement | Method to determine structure: ![]() Starting model: ensemble of 2byn, 2byr, 2bys, and 2pgz Resolution: 2.05→49.149 Å / SU ML: 0.24 / Cross valid method: NONE / σ(F): 1.34 / Phase error: 23.82 / 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 max: 65.88 Å2 / Biso mean: 22.2867 Å2 / Biso min: 10.93 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.05→49.149 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14 / % reflection obs: 100 %
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