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Yorodumi- PDB-5oin: InhA (T2A mutant) complexed with N-(1-(pyrimidin-2-yl)piperidin-4... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5oin | ||||||
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Title | InhA (T2A mutant) complexed with N-(1-(pyrimidin-2-yl)piperidin-4-yl)acetamide | ||||||
Components | Enoyl-[acyl-carrier-protein] reductase [NADH] | ||||||
Keywords | OXIDOREDUCTASE / Inhibitor / complex / fragment based drug discovery / tuberculosis | ||||||
Function / homology | Function and homology information trans-2-enoyl-CoA reductase (NADH) activity / mycolic acid biosynthetic process / fatty acid elongation / enoyl-[acyl-carrier-protein] reductase (NADH) / enoyl-[acyl-carrier-protein] reductase (NADH) activity / NAD+ binding / peptidoglycan-based cell wall / fatty acid binding / response to antibiotic / plasma membrane Similarity search - Function | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.82 Å | ||||||
Authors | Convery, M.A. | ||||||
Citation | Journal: ChemMedChem / Year: 2018 Title: Screening of a Novel Fragment Library with Functional Complexity against Mycobacterium tuberculosis InhA. Authors: Prati, F. / Zuccotto, F. / Fletcher, D. / Convery, M.A. / Fernandez-Menendez, R. / Bates, R. / Encinas, L. / Zeng, J. / Chung, C.W. / De Dios Anton, P. / Mendoza-Losana, A. / Mackenzie, C. / ...Authors: Prati, F. / Zuccotto, F. / Fletcher, D. / Convery, M.A. / Fernandez-Menendez, R. / Bates, R. / Encinas, L. / Zeng, J. / Chung, C.W. / De Dios Anton, P. / Mendoza-Losana, A. / Mackenzie, C. / Green, S.R. / Huggett, M. / Barros, D. / Wyatt, P.G. / Ray, P.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5oin.cif.gz | 405.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5oin.ent.gz | 352 KB | Display | PDB format |
PDBx/mmJSON format | 5oin.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oi/5oin ftp://data.pdbj.org/pub/pdb/validation_reports/oi/5oin | HTTPS FTP |
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-Related structure data
Related structure data | 5oicC 5oifC 5oilC 5oimC 5oioC 5oipC 5oiqC 5oirC 5oisC 5oitC C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 28524.754 Da / Num. of mol.: 4 / Mutation: T2A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria) Strain: ATCC 25618 / H37Rv / Gene: inhA, Rv1484, MTCY277.05 / Production host: Escherichia coli (E. coli) References: UniProt: P9WGR1, enoyl-[acyl-carrier-protein] reductase (NADH) #2: Chemical | ChemComp-NAD / #3: Chemical | #4: 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: 3.81 Å3/Da / Density % sol: 67.74 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 35-42% Ethoxyethanol and 0.1M Mes pH 6.5-6.8. 5% glycerol used as cryoprotectant. Crystals were soaked to obtain ligand complex. PH range: 6.5-6.8 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 9, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Resolution: 2.82→82.6 Å / Num. obs: 42892 / % possible obs: 100 % / Redundancy: 6.6 % / Biso Wilson estimate: 80.56 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.123 / Net I/σ(I): 11.3 |
Reflection shell | Resolution: 2.82→2.89 Å / Redundancy: 6.6 % / Rmerge(I) obs: 2.08 / Num. unique obs: 3145 / CC1/2: 0.474 / % possible all: 100 |
-Processing
Software |
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Refinement | Resolution: 2.82→82.6 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.955 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.401 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.391 / SU Rfree Blow DPI: 0.224 / SU Rfree Cruickshank DPI: 0.228
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Displacement parameters | Biso mean: 86.68 Å2
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Refine analyze | Luzzati coordinate error obs: 0.33 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.82→82.6 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.82→2.89 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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