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Yorodumi- PDB-1p45: Targeting tuberculosis and malaria through inhibition of enoyl re... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1p45 | ||||||
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Title | Targeting tuberculosis and malaria through inhibition of enoyl reductase: compound activity and structural data | ||||||
Components | Enoyl-[acyl-carrier-protein] reductase [NADH] | ||||||
Keywords | OXIDOREDUCTASE / InhA / short chain dehydrogenase reductase / triclosan / rossmann fold / enoyl-ACP reductase / Structural Genomics / PSI / Protein Structure Initiative / TB Structural Genomics Consortium / TBSGC | ||||||
Function / homology | Function and homology information enoyl-[acyl-carrier-protein] reductase activity (NAD(P)H) / 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 / fatty acid biosynthetic process ...enoyl-[acyl-carrier-protein] reductase activity (NAD(P)H) / 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 / fatty acid biosynthetic process / response to antibiotic / plasma membrane Similarity search - Function | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Kuo, M.R. / Morbidoni, H.R. / Alland, D. / Sneddon, S.F. / Gourlie, B.B. / Staveski, M.M. / Leonard, M. / Gregory, J.S. / Janjigian, A.D. / Yee, C. ...Kuo, M.R. / Morbidoni, H.R. / Alland, D. / Sneddon, S.F. / Gourlie, B.B. / Staveski, M.M. / Leonard, M. / Gregory, J.S. / Janjigian, A.D. / Yee, C. / Musser, J.M. / Kreiswirth, B.N. / Iwamoto, H. / Perozzo, R. / Jacobs Jr., W.R. / Sacchettini, J.C. / Fidock, D.A. / TB Structural Genomics Consortium (TBSGC) | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2003 Title: Targeting tuberculosis and malaria through inhibition of Enoyl reductase: compound activity and structural data. Authors: Kuo, M.R. / Morbidoni, H.R. / Alland, D. / Sneddon, S.F. / Gourlie, B.B. / Staveski, M.M. / Leonard, M. / Gregory, J.S. / Janjigian, A.D. / Yee, C. / Musser, J.M. / Kreiswirth, B. / Iwamoto, ...Authors: Kuo, M.R. / Morbidoni, H.R. / Alland, D. / Sneddon, S.F. / Gourlie, B.B. / Staveski, M.M. / Leonard, M. / Gregory, J.S. / Janjigian, A.D. / Yee, C. / Musser, J.M. / Kreiswirth, B. / Iwamoto, H. / Perozzo, R. / Jacobs, W.R. / Sacchettini, J.C. / Fidock, D.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1p45.cif.gz | 111 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1p45.ent.gz | 91.9 KB | Display | PDB format |
PDBx/mmJSON format | 1p45.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p4/1p45 ftp://data.pdbj.org/pub/pdb/validation_reports/p4/1p45 | HTTPS FTP |
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-Related 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: 28554.781 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: INHA OR RV1484 OR MT1531 OR MTCY277.05 / Production host: Escherichia coli (E. coli) References: UniProt: P0A5Y6, UniProt: P9WGR1*PLUS, 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: 4.1 Å3/Da / Density % sol: 69.99 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 100 mM Tris, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 291K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 6.8 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD |
Radiation | Monochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→30 Å / Num. obs: 27704 / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
Reflection | *PLUS % possible obs: 95.1 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.08 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→30 Å / SU B: 12.02 / SU ML: 0.249 / Cross valid method: THROUGHOUT / ESU R: 0.4 / ESU R Free: 0.311 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 50.889 Å2
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Refinement step | Cycle: LAST / Resolution: 2.6→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.603→2.67 Å / Total num. of bins used: 20 /
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Software | *PLUS Version: 5.1.24 / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.6 Å / Num. reflection obs: 27704 / % reflection Rfree: 10 % / Rfactor Rfree: 0.282 / Rfactor Rwork: 0.225 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |