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Yorodumi- PDB-5oif: InhA (T2A mutant) complexed with 1-benzyl-3-methyl-1H-pyrazol-5-amine -
+Open data
-Basic information
Entry | Database: PDB / ID: 5oif | ||||||
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Title | InhA (T2A mutant) complexed with 1-benzyl-3-methyl-1H-pyrazol-5-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: 2.03 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 | 5oif.cif.gz | 210 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5oif.ent.gz | 177.5 KB | Display | PDB format |
PDBx/mmJSON format | 5oif.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oi/5oif ftp://data.pdbj.org/pub/pdb/validation_reports/oi/5oif | HTTPS FTP |
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-Related structure data
Related structure data | 5oicC 5oilC 5oimC 5oinC 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.: 2 / 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 | #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: 2.33 Å3/Da / Density % sol: 47.2 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 2.17% MPD, 0.3M Mg(NO3)2, 0.1M Tris pH8 and 20% PEG2K Cryo - well soln |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9797 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 5, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9797 Å / Relative weight: 1 |
Reflection | Resolution: 2.03→56.93 Å / Num. obs: 32020 / % possible obs: 95.1 % / Redundancy: 3.3 % / Biso Wilson estimate: 27.75 Å2 / CC1/2: 0.976 / Rmerge(I) obs: 0.036 / Net I/σ(I): 7.2 |
Reflection shell | Resolution: 2.03→2.08 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.812 / Num. unique obs: 2444 / CC1/2: 0.531 / Χ2: 1.5 / % possible all: 98.2 |
-Processing
Software |
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Refinement | Resolution: 2.03→26.58 Å / Cor.coef. Fo:Fc: 0.9331 / Cor.coef. Fo:Fc free: 0.9013 / SU R Cruickshank DPI: 0.195 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.199 / SU Rfree Blow DPI: 0.168 / SU Rfree Cruickshank DPI: 0.168
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Displacement parameters | Biso mean: 28.9 Å2
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Refine analyze | Luzzati coordinate error obs: 0.237 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.03→26.58 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.03→2.1 Å / Total num. of bins used: 16
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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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