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- PDB-6w29: Trypanosoma cruzi Malic Enzyme in complex with inhibitor (MEC013) -
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Open data
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Basic information
Entry | Database: PDB / ID: 6w29 | ||||||||||||
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Title | Trypanosoma cruzi Malic Enzyme in complex with inhibitor (MEC013) | ||||||||||||
![]() | Malic enzyme![]() | ||||||||||||
![]() | OXIDOREDUCTASE/Inhibitor / Inhibitor / ![]() ![]() | ||||||||||||
Function / homology | ![]() malate dehydrogenase (decarboxylating) (NAD+) activity / malate metabolic process / pyruvate metabolic process / NAD binding / ![]() ![]() ![]() 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 | ![]() | 124.8 KB | Display | ![]() |
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PDB format | ![]() | 93 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6w2nC ![]() 6w49C ![]() 6w53C ![]() 6w56C ![]() 6w57C ![]() 6w59C ![]() 7mf4C ![]() 1gq2S ![]() 1gz3S ![]() 3wjaS 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
-Protein , 1 types, 1 molecules A
#1: Protein | ![]() Mass: 61610.406 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() Strain: CL Brener / Gene: Tc00.1047053505183.30 / Plasmid: pET_SUMO / Production host: ![]() ![]() ![]() |
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-Non-polymers , 5 types, 78 molecules ![](data/chem/img/SEV.gif)
![](data/chem/img/CIT.gif)
![](data/chem/img/EPE.gif)
![](data/chem/img/DMS.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CIT.gif)
![](data/chem/img/EPE.gif)
![](data/chem/img/DMS.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-SEV / |
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#3: Chemical | ChemComp-CIT / ![]() |
#4: Chemical | ChemComp-EPE / ![]() |
#5: Chemical | ChemComp-DMS / ![]() |
#6: Water | ChemComp-HOH / ![]() |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.56 Å3/Da / Density % sol: 52.01 % |
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Crystal grow![]() | Temperature: 291 K / Method: vapor diffusion, hanging drop / Details: 0.1 M HEPES, 1.2-1.4 M Na3-Citrate / PH range: 6.8 -7.2 |
-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: Mar 14, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.14→47.54 Å / Num. obs: 36499 / % possible obs: 99.9 % / Redundancy: 11.1 % / CC1/2: 0.998 / Rmerge(I) obs: 0.13 / Rpim(I) all: 0.04 / Rrim(I) all: 0.136 / Net I/σ(I): 13 |
Reflection shell | Resolution: 2.14→2.2 Å / Redundancy: 4.8 % / Rmerge(I) obs: 1.054 / Num. measured all: 13953 / Num. unique obs: 2879 / CC1/2: 0.53 / Rpim(I) all: 0.509 / Rrim(I) all: 1.18 / Net I/σ(I) obs: 1.3 / % possible all: 98.8 |
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Processing
Software |
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Refinement | Method to determine structure![]() ![]() Starting model: 1GZ3, 3WJA, 1GQ2 Resolution: 2.14→47.54 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.932 / SU B: 6.534 / SU ML: 0.157 / SU R Cruickshank DPI: 0.2287 / Cross valid method: FREE R-VALUE / σ(F): 0 / ESU R: 0.229 / ESU R Free: 0.186
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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: 126.97 Å2 / Biso mean: 40.258 Å2 / Biso min: 23.09 Å2
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Refinement step | Cycle: final / Resolution: 2.14→47.54 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.14→2.196 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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