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Yorodumi- PDB-5oit: InhA (T2A mutant) complexed with 5-((5-Amino-3-methyl-1H-pyrazol-... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5oit | ||||||
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Title | InhA (T2A mutant) complexed with 5-((5-Amino-3-methyl-1H-pyrazol-1-yl)methyl)-N-(1-(2-chloro-6-fluorobenzyl)-1H-pyrazol-3-yl)-1,3,4-thiadiazol-2-amine | ||||||
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: 2.58 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 | 5oit.cif.gz | 429 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5oit.ent.gz | 357.7 KB | Display | PDB format |
PDBx/mmJSON format | 5oit.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5oit_validation.pdf.gz | 2.9 MB | Display | wwPDB validaton report |
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Full document | 5oit_full_validation.pdf.gz | 2.9 MB | Display | |
Data in XML | 5oit_validation.xml.gz | 42.8 KB | Display | |
Data in CIF | 5oit_validation.cif.gz | 60.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oi/5oit ftp://data.pdbj.org/pub/pdb/validation_reports/oi/5oit | HTTPS FTP |
-Related structure data
Related structure data | 5oicC 5oifC 5oilC 5oimC 5oinC 5oioC 5oipC 5oiqC 5oirC 5oisC 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 (bacteria) / Gene: inhA, Rv1484, MTCY277.05 / Production host: Escherichia coli (E. coli) References: UniProt: P9WGR1, enoyl-[acyl-carrier-protein] reductase (NADH) #2: Chemical | ChemComp-9WH / #3: Chemical | ChemComp-NAD / #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: 4.28 Å3/Da / Density % sol: 71.29 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.2M Ammonium Sulfate, 30% PEG4K. Cryo - well + 30% ethylene glycol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 19, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.58→68.5 Å / Num. obs: 62385 / % possible obs: 99.9 % / Redundancy: 6.7 % / Biso Wilson estimate: 75.08 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.14 / Net I/σ(I): 11.3 |
Reflection shell | Resolution: 2.58→2.65 Å / Redundancy: 7 % / Rmerge(I) obs: 2.019 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 4549 / CC1/2: 0.515 / % possible all: 99.6 |
-Processing
Software |
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Refinement | Resolution: 2.58→68.5 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.935 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.244 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.252 / SU Rfree Blow DPI: 0.192 / SU Rfree Cruickshank DPI: 0.192
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Displacement parameters | Biso mean: 63.62 Å2
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Refine analyze | Luzzati coordinate error obs: 0.3 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.58→68.5 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.58→2.65 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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