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Yorodumi- PDB-4uvd: Discovery of pyrimidine isoxazoles InhA in complex with compound 6 -
+Open data
-Basic information
Entry | Database: PDB / ID: 4uvd | ||||||
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Title | Discovery of pyrimidine isoxazoles InhA in complex with compound 6 | ||||||
Components | ENOYL-[ACYL-CARRIER-PROTEIN] REDUCTASE [NADH] | ||||||
Keywords | OXIDOREDUCTASE / INHA / ACP ENOYL REDUCTASE / FBLG / PYRIMIDINE ISOXAZOLE | ||||||
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 / 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: 1.82 Å | ||||||
Authors | Read, J.A. / Gingell, H. / Madhavapeddi, P. / Ghorpade, S. / Cowan, S. | ||||||
Citation | Journal: To be Published Title: Hitting the Target in More Than One Way: Novel, Direct Inhibitors of Mycobacterium Tuberculosis Enoyl Acp Reductase Authors: Madhavapeddi, P. / Kale, R.R. / Cowen, S.D. / Ghorpade, S.R. / Davies, G. / Bellale, E.V. / Kale, M.G. / Srivastava, A. / Spadola, L. / Kawatkar, A. / Raichurkar, A.V. / Tonge, M. / ...Authors: Madhavapeddi, P. / Kale, R.R. / Cowen, S.D. / Ghorpade, S.R. / Davies, G. / Bellale, E.V. / Kale, M.G. / Srivastava, A. / Spadola, L. / Kawatkar, A. / Raichurkar, A.V. / Tonge, M. / Nandishaiah, R. / Guptha, S. / Narayan, A. / Gingell, H. / Plant, D. / Landge, S. / Menasinakai, S. / Prabhakar, K.R. / Achar, V. / Ambady, A. / Sambandamurthy, V.K. / Ramachandran, V. / Panduga, V. / Reddy, J. / Kumar, C.N.N. / Kaur, P. / Shandil, R. / Iyer, P.S. / Narayanan, S. / Read, J.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4uvd.cif.gz | 113.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4uvd.ent.gz | 94.9 KB | Display | PDB format |
PDBx/mmJSON format | 4uvd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uv/4uvd ftp://data.pdbj.org/pub/pdb/validation_reports/uv/4uvd | HTTPS FTP |
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-Related structure data
Related structure data | 4uveC 4uvgC 4uvhC 4uviC 40drS C: citing same article (ref.) S: Starting model for refinement |
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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 on special symmetry positions |
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-Components
#1: Protein | Mass: 28554.781 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) MYCOBACTERIUM TUBERCULOSIS (bacteria) / Strain: H37RV / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): STAR References: UniProt: M9TGV3, UniProt: P9WGR1*PLUS, enoyl-[acyl-carrier-protein] reductase (NADH) |
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#2: Chemical | ChemComp-NAD / |
#3: Chemical | ChemComp-MG / |
#4: Chemical | ChemComp-HRW / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.35 Å3/Da / Density % sol: 63.31 % / Description: NONE |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Sep 19, 2012 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92 Å / Relative weight: 1 |
Reflection | Resolution: 1.82→72.2 Å / Num. obs: 35577 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 8.1 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 28.3 |
Reflection shell | Resolution: 1.82→1.92 Å / Redundancy: 8.3 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 4.4 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 40DR Resolution: 1.82→72.18 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.959 / SU B: 3.094 / SU ML: 0.052 / Cross valid method: THROUGHOUT / ESU R: 0.092 / ESU R Free: 0.089 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.736 Å2
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Refinement step | Cycle: LAST / Resolution: 1.82→72.18 Å
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Refine LS restraints |
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