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- PDB-5tym: alpha-esterase-7 in complex with [3-bromo-5-(pyrrolidin-1-yl)phen... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5tym | ||||||
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Title | alpha-esterase-7 in complex with [3-bromo-5-(pyrrolidin-1-yl)phenyl]borinic acid | ||||||
![]() | Carboxylic ester hydrolase | ||||||
![]() | hydrolase/hydrolase inhibitor / carboxylesterase / insecticide resistance / covalent inhibitor / organophosphate / hydrolase-hydrolase inhibitor complex | ||||||
Function / homology | ![]() Hydrolases; Acting on ester bonds; Carboxylic-ester hydrolases / carboxylic ester hydrolase activity Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Correy, G.J. / Jackson, C.J. | ||||||
![]() | ![]() Title: Overcoming insecticide resistance through computational inhibitor design. Authors: Correy, G.J. / Zaidman, D. / Harmelin, A. / Carvalho, S. / Mabbitt, P.D. / Calaora, V. / James, P.J. / Kotze, A.C. / Jackson, C.J. / London, N. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 129.6 KB | Display | ![]() |
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PDB format | ![]() | 99 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 746 KB | Display | ![]() |
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Full document | ![]() | 752.3 KB | Display | |
Data in XML | ![]() | 22.7 KB | Display | |
Data in CIF | ![]() | 31.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5tyjC ![]() 5tykC ![]() 5tylC ![]() 5tynC ![]() 5tyoC ![]() 5typC ![]() 5ch3S C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 66412.922 Da / Num. of mol.: 1 / Mutation: D83A, K530E Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: LcaE7 / Production host: ![]() ![]() References: UniProt: Q25252, Hydrolases; Acting on ester bonds; Carboxylic-ester hydrolases |
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#2: Chemical | ChemComp-7NS / [ |
#3: Water | ChemComp-HOH / |
Has protein modification | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.09 Å3/Da / Density % sol: 41.04 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 5.1 / Details: 100 mM sodium acetate pH 5.1, 15% PEG 550 MME |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Sep 27, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 1.84→38 Å / Num. obs: 48767 / % possible obs: 99.9 % / Redundancy: 11.9 % / Rsym value: 0.14 / Net I/σ(I): 12.4 |
Reflection shell | Resolution: 1.84→1.88 Å / Redundancy: 10.9 % / Rmerge(I) obs: 2.48 / Mean I/σ(I) obs: 1.1 / Num. unique all: 4823 / CC1/2: 0.326 / % possible all: 99.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5CH3 Resolution: 1.84→38.017 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 32.36 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.84→38.017 Å
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Refine LS restraints |
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LS refinement shell |
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