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- PDB-5brd: Crystal structure of Trypanosoma cruzi glucokinase in complex wit... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5brd | |||||||||
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Title | Crystal structure of Trypanosoma cruzi glucokinase in complex with inhibitor BENZ-GlcN | |||||||||
![]() | Glucokinase 1, putative | |||||||||
![]() | Transferase/Transferase Inhibitor / Transferase / Hexose Kinase / Transferase-Transferase Inhibitor complex | |||||||||
Function / homology | ![]() glucokinase / glucokinase activity / D-glucose binding / glycolytic process / ATP binding Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() ![]() | |||||||||
![]() | D'Antonio, E.L. / Perry, K. / Deinema, M.S. / Kearns, S.P. / Frey, T.A. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structure-based approach to the identification of a novel group of selective glucosamine analogue inhibitors of Trypanosoma cruzi glucokinase. Authors: D'Antonio, E.L. / Deinema, M.S. / Kearns, S.P. / Frey, T.A. / Tanghe, S. / Perry, K. / Roy, T.A. / Gracz, H.S. / Rodriguez, A. / D'Antonio, J. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 157.1 KB | Display | ![]() |
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PDB format | ![]() | 122.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 994.7 KB | Display | ![]() |
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Full document | ![]() | 1001.2 KB | Display | |
Data in XML | ![]() | 27.5 KB | Display | |
Data in CIF | ![]() | 37.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5breC ![]() 5brfC ![]() 5brhC ![]() 2q2rS 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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Unit cell |
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Components
#1: Protein | Mass: 42226.648 Da / Num. of mol.: 2 / Fragment: UNP residues 1-367 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: CL Brener / Gene: Tc00.1047053510187.100 / Plasmid: pET-28a(+) / Production host: ![]() ![]() #2: Sugar | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.54 Å3/Da / Density % sol: 51.55 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7 Details: A glucose-free TcGlcK crystal was soaked in 1.0 mM BENZ-GlcN, 5.0% (v/v) DMSO, 0.1 M sodium citrate (pH 7.0), 20% (w/v) PEG 3,350 for 28 hours |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||
Detector | Type: ADSC HF-4M / Detector: PIXEL / Date: Feb 15, 2015 / Details: ADSC HF-4M PIXEL ARRAY DETECTOR | |||||||||||||||||||||||||||
Radiation | Monochromator: Cryogenically-cooled single crystal Si(220) side bounce monochromator Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 | |||||||||||||||||||||||||||
Reflection | Resolution: 2.4→76.37 Å / Num. obs: 31494 / % possible obs: 98.5 % / Redundancy: 4.3 % / Biso Wilson estimate: 51.07 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.079 / Rpim(I) all: 0.041 / Net I/σ(I): 12.9 / Num. measured all: 136171 | |||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 2Q2R Resolution: 2.4→49.056 Å / FOM work R set: 0.785 / SU ML: 0.4 / Cross valid method: THROUGHOUT / σ(F): 1.93 / Phase error: 28.77 / 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: 111.01 Å2 / Biso mean: 42.51 Å2 / Biso min: 5.34 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.4→49.056 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: 22
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