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- PDB-5gn7: Crystal structure of alternative oxidase from Trypanosoma brucei ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5gn7 | ||||||
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Title | Crystal structure of alternative oxidase from Trypanosoma brucei brucei complexed with cumarin derivative-17 | ||||||
![]() | Alternative oxidase, mitochondrial | ||||||
![]() | TRANSFERASE / Alternative oxidase / inhibitor / drug / African trypanosomes / OXIDO-REDUCTASE | ||||||
Function / homology | ![]() alternative oxidase activity / alternative respiration / Oxidoreductases / : / ferric iron binding / mitochondrial inner membrane / oxidoreductase activity / mitochondrion Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Balogun, E.O. / Inaoka, D.K. / Shiba, T. / Tsuge, T. / May, B. / Sato, T. / Kido, Y. / Takeshi, N. / Aoki, T. / Honma, T. ...Balogun, E.O. / Inaoka, D.K. / Shiba, T. / Tsuge, T. / May, B. / Sato, T. / Kido, Y. / Takeshi, N. / Aoki, T. / Honma, T. / Tanaka, A. / Inoue, M. / Matsuoka, S. / Michels, P.A.M. / Watanabe, Y. / Moore, A.L. / Harada, S. / Kita, K. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Discovery of trypanocidal coumarins with dual inhibition of both the glycerol kinase and alternative oxidase ofTrypanosoma brucei brucei. Authors: Balogun, E.O. / Inaoka, D.K. / Shiba, T. / Tsuge, C. / May, B. / Sato, T. / Kido, Y. / Nara, T. / Aoki, T. / Honma, T. / Tanaka, A. / Inoue, M. / Matsuoka, S. / Michels, P.A.M. / Watanabe, Y. ...Authors: Balogun, E.O. / Inaoka, D.K. / Shiba, T. / Tsuge, C. / May, B. / Sato, T. / Kido, Y. / Nara, T. / Aoki, T. / Honma, T. / Tanaka, A. / Inoue, M. / Matsuoka, S. / Michels, P.A.M. / Watanabe, Y.I. / Moore, A.L. / Harada, S. / Kita, K. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 227 KB | Display | ![]() |
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PDB format | ![]() | 180.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 726.7 KB | Display | ![]() |
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Full document | ![]() | 751.3 KB | Display | |
Data in XML | ![]() | 38.5 KB | Display | |
Data in CIF | ![]() | 52.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5gn5C ![]() 5gn6C ![]() 5gn9C ![]() 3vv9S 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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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 37643.289 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-FE / #3: Chemical | ChemComp-6XZ / | #4: Chemical | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.21 Å3/Da / Density % sol: 61.69 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 30% PEG 400, 0.1M IMIDAZOLE, 0.5M POTASSIUM FORMATE PH range: 7.3-7.7 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Dec 2, 2014 | |||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 | |||||||||||||||
Reflection twin |
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Reflection | Resolution: 3.2→50 Å / Num. obs: 31113 / % possible obs: 94.3 % / Redundancy: 2.8 % / Rmerge(I) obs: 0.079 / Net I/σ(I): 9 | |||||||||||||||
Reflection shell | Resolution: 3.2→3.26 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.661 / Mean I/σ(I) obs: 1.59 / % possible all: 92.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3VV9 Resolution: 3.2→45.54 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.887 / SU B: 15.915 / SU ML: 0.294 / Cross valid method: THROUGHOUT / ESU R Free: 0.113 / 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 |
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Refinement step | Cycle: 1 / Resolution: 3.2→45.54 Å
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Refine LS restraints |
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