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Yorodumi- PDB-5l8a: Targeting the PEX14-PEX5 interaction by small molecules provides ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5l8a | ||||||
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Title | Targeting the PEX14-PEX5 interaction by small molecules provides novel therapeutic routes to treat trypanosomiases. | ||||||
Components | Peroxin 14 | ||||||
Keywords | SIGNALING PROTEIN / trypanosomiasis / glycosome / protein-protein interaction inhibitor / structure-based drug discovery / inhibitor | ||||||
Function / homology | Function and homology information glycosome membrane / protein import into peroxisome matrix, docking / protein targeting to vacuole / glycosome / post-transcriptional regulation of gene expression Similarity search - Function | ||||||
Biological species | Trypanosoma brucei brucei (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.57 Å | ||||||
Authors | Dawidowski, M. / Emmanouilidis, L. / Sattler, M. / Popowicz, G.M. | ||||||
Citation | Journal: Science / Year: 2017 Title: Inhibitors of PEX14 disrupt protein import into glycosomes and kill Trypanosoma parasites. Authors: Dawidowski, M. / Emmanouilidis, L. / Kalel, V.C. / Tripsianes, K. / Schorpp, K. / Hadian, K. / Kaiser, M. / Maser, P. / Kolonko, M. / Tanghe, S. / Rodriguez, A. / Schliebs, W. / Erdmann, R. ...Authors: Dawidowski, M. / Emmanouilidis, L. / Kalel, V.C. / Tripsianes, K. / Schorpp, K. / Hadian, K. / Kaiser, M. / Maser, P. / Kolonko, M. / Tanghe, S. / Rodriguez, A. / Schliebs, W. / Erdmann, R. / Sattler, M. / Popowicz, G.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5l8a.cif.gz | 130.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5l8a.ent.gz | 101.4 KB | Display | PDB format |
PDBx/mmJSON format | 5l8a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l8/5l8a ftp://data.pdbj.org/pub/pdb/validation_reports/l8/5l8a | HTTPS FTP |
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-Related structure data
Related structure data | 5l87C 5mmcC 5n8vC 3ff5S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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4 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 0 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: SER / End label comp-ID: SER / Refine code: 0 / Auth seq-ID: 5 - 66 / Label seq-ID: 8 - 69
NCS ensembles :
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-Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 7883.075 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Trypanosoma brucei brucei (eukaryote) / Gene: PEX14 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8IEW2 |
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-Non-polymers , 5 types, 283 molecules
#2: Chemical | ChemComp-6RB / #3: Chemical | ChemComp-GLY / | #4: Chemical | ChemComp-NA / | #5: Chemical | ChemComp-EDO / | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.15 Å3/Da / Density % sol: 42.91 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, sitting drop / Details: 0.1 M SPG Buffer pH6 25% PEG 1500 |
-Data collection
Diffraction | Mean temperature: 90 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.8726 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 27, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8726 Å / Relative weight: 1 |
Reflection | Resolution: 1.57→31.3 Å / Num. obs: 33844 / % possible obs: 92.7 % / Redundancy: 3.6 % / Net I/σ(I): 7.5 |
Reflection shell | Resolution: 1.57→1.66 Å / Rmerge(I) obs: 0.603 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3FF5 Resolution: 1.57→27.79 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.916 / SU B: 5.226 / SU ML: 0.084 / Cross valid method: THROUGHOUT / ESU R: 0.147 / ESU R Free: 0.112 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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 mean: 19.175 Å2
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Refinement step | Cycle: 1 / Resolution: 1.57→27.79 Å
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Refine LS restraints |
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