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Yorodumi- PDB-6sq5: Crystal structure of M. tuberculosis InhA in complex with NAD+ an... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6sq5 | |||||||||
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Title | Crystal structure of M. tuberculosis InhA in complex with NAD+ and 3-[3-(trifluoromethyl)phenyl]prop-2-enoic acid | |||||||||
Components | Enoyl-[acyl-carrier-protein] reductase [NADH] | |||||||||
Keywords | OXIDOREDUCTASE / InhA / NADH-dependent enoyl-[acyl-carrier-protein] reductase | |||||||||
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 / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.84 Å | |||||||||
Authors | Mendes, V. / Sabbah, M. / Coyne, A.G. / Abell, C. / Blundell, T.L. | |||||||||
Funding support | United Kingdom, United States, 2items
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Citation | Journal: J.Med.Chem. / Year: 2020 Title: Fragment-Based Design ofMycobacterium tuberculosisInhA Inhibitors. Authors: Sabbah, M. / Mendes, V. / Vistal, R.G. / Dias, D.M.G. / Zahorszka, M. / Mikusova, K. / Kordulakova, J. / Coyne, A.G. / Blundell, T.L. / Abell, C. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6sq5.cif.gz | 121 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6sq5.ent.gz | 92.6 KB | Display | PDB format |
PDBx/mmJSON format | 6sq5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6sq5_validation.pdf.gz | 979.2 KB | Display | wwPDB validaton report |
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Full document | 6sq5_full_validation.pdf.gz | 983.5 KB | Display | |
Data in XML | 6sq5_validation.xml.gz | 13.8 KB | Display | |
Data in CIF | 6sq5_validation.cif.gz | 19.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sq/6sq5 ftp://data.pdbj.org/pub/pdb/validation_reports/sq/6sq5 | HTTPS FTP |
-Related structure data
Related structure data | 6sq7C 6sq9C 6sqbC 6sqdC 6sqlC 2b35S S: Starting model for refinement 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 28641.857 Da / Num. of mol.: 1 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 BL21(DE3) (bacteria) References: UniProt: P9WGR1, enoyl-[acyl-carrier-protein] reductase (NADH) |
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#2: Chemical | ChemComp-NAD / |
#3: Chemical | ChemComp-LRW / (~{ |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.36 Å3/Da / Density % sol: 63.41 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 0.1 M HEPES pH 7.0 0.1 M sodium acetate 25-30% PEG 400 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 Å | |||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 21, 2014 | |||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97625 Å / Relative weight: 1 | |||||||||||||||||||||||||||
Reflection | Resolution: 1.837→140.23 Å / Num. obs: 35046 / % possible obs: 100 % / Redundancy: 19.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.062 / Rpim(I) all: 0.015 / Rrim(I) all: 0.063 / Net I/σ(I): 26.4 | |||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / % possible all: 100
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2B35 Resolution: 1.84→72.354 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 17.68
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 126.42 Å2 / Biso mean: 46.8417 Å2 / Biso min: 26.04 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.84→72.354 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %
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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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