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- PDB-6w56: Trypanosoma cruzi Malic Enzyme in complex with inhibitor (MEC062) -
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Open data
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Basic information
Entry | Database: PDB / ID: 6w56 | ||||||||||||
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Title | Trypanosoma cruzi Malic Enzyme in complex with inhibitor (MEC062) | ||||||||||||
![]() | Malic enzyme | ||||||||||||
![]() | OXIDOREDUCTASE/Inhibitor / Inhibitor / OXIDOREDUCTASE / OXIDOREDUCTASE-Inhibitor complex | ||||||||||||
Function / homology | ![]() malate dehydrogenase (decarboxylating) (NAD+) activity / malate metabolic process / pyruvate metabolic process / NAD binding / mitochondrion / metal ion binding / cytosol Similarity search - Function | ||||||||||||
Biological species | ![]() ![]() | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Mercaldi, G.F. / Fagundes, M. / Faria, J.N. / Cordeiro, A.T. | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Trypanosoma cruzi Malic Enzyme Is the Target for Sulfonamide Hits from the GSK Chagas Box. Authors: Mercaldi, G.F. / Eufrasio, A.G. / Ranzani, A.T. / do Nascimento Faria, J. / Mota, S.G.R. / Fagundes, M. / Bruder, M. / Cordeiro, A.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 | ![]() | 131 KB | Display | ![]() |
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PDB format | ![]() | 97.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6w29SC ![]() 6w2nC ![]() 6w49C ![]() 6w53C ![]() 6w57C ![]() 6w59C ![]() 7mf4C 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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1 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 61610.406 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Chemical | ChemComp-EPE / |
#3: Chemical | ChemComp-SZJ / ~{ |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.55 Å3/Da / Density % sol: 51.8 % / Mosaicity: 0.27 ° |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.1 M HEPES, 1.2-1.4 M Na3-Citrate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jul 24, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.4587 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→47.41 Å / Num. obs: 50906 / % possible obs: 99.3 % / Redundancy: 6 % / CC1/2: 0.998 / Rmerge(I) obs: 0.082 / Rpim(I) all: 0.035 / Rrim(I) all: 0.089 / Net I/σ(I): 12.6 / Num. measured all: 303517 / Scaling rejects: 13 |
Reflection shell | Resolution: 1.9→1.94 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.719 / Num. measured all: 12061 / Num. unique obs: 3215 / CC1/2: 0.641 / Rpim(I) all: 0.404 / Rrim(I) all: 0.83 / Net I/σ(I) obs: 1.6 / % possible all: 98.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6w29 Resolution: 1.9→36.27 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.953 / SU B: 3.159 / SU ML: 0.09 / SU R Cruickshank DPI: 0.1385 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.139 / ESU R Free: 0.121 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 96.58 Å2 / Biso mean: 29.678 Å2 / Biso min: 17.06 Å2
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Refinement step | Cycle: final / Resolution: 1.9→36.27 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.949 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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