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- PDB-5edt: Crystal structure of Mycobacterium tuberculosis CYP121 in complex... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5edt | |||||||||
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Title | Crystal structure of Mycobacterium tuberculosis CYP121 in complex with LIG9 | |||||||||
![]() | Cytochrome P450 121 | |||||||||
![]() | OXIDOREDUCTASE / cytochrome P450 / CYP121 / Mycobacterium tuberculosis / fragment-based drug discovery | |||||||||
Function / homology | ![]() Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / monooxygenase activity / iron ion binding / heme binding / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Kavanagh, M.E. / Coyne, A.G. / McLean, K.J. / James, G.G. / Levy, C. / Marino, L.B. / Carvalho, L.P.D. / Chan, D.S.H. / Hudson, S.A. / Surade, S. ...Kavanagh, M.E. / Coyne, A.G. / McLean, K.J. / James, G.G. / Levy, C. / Marino, L.B. / Carvalho, L.P.D. / Chan, D.S.H. / Hudson, S.A. / Surade, S. / Munro, A.W. / Abell, C. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Fragment-Based Approaches to the Development of Mycobacterium tuberculosis CYP121 Inhibitors. Authors: Kavanagh, M.E. / Coyne, A.G. / McLean, K.J. / James, G.G. / Levy, C.W. / Marino, L.B. / de Carvalho, L.P. / Chan, D.S. / Hudson, S.A. / Surade, S. / Leys, D. / Munro, A.W. / Abell, C. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 98.9 KB | Display | ![]() |
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PDB format | ![]() | 72.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 814.8 KB | Display | ![]() |
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Full document | ![]() | 820.6 KB | Display | |
Data in XML | ![]() | 19.2 KB | Display | |
Data in CIF | ![]() | 27.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5ibdC ![]() 5ibeC ![]() 5ibfC ![]() 5ibgC ![]() 5ibhC ![]() 5ibiC ![]() 5ibjC ![]() 4ktfS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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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: 43174.668 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: cyp121, Mb2299 / Production host: ![]() ![]() References: UniProt: P0A515, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen | ||
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#2: Chemical | ChemComp-HEM / | ||
#3: Chemical | ChemComp-5MK / | ||
#4: Chemical | ChemComp-SO4 / #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.61 Å3/Da / Density % sol: 52.81 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 2M AMMONIUM SULFATE, 0.1M SODIUM CACODYLATE |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: Bruker Platinum 135 / Detector: CCD / Date: Sep 15, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.45→7.1 Å / Num. all: 591452 / Num. obs: 18202 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 32 % / Rsym value: 0.08 / Net I/σ(I): 16 |
Reflection shell | Resolution: 2.45→2.51 Å / Redundancy: 9.77 % / % possible all: 99.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4KTF Resolution: 2.45→7.1 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.894 / SU B: 7.836 / SU ML: 0.177 / Cross valid method: THROUGHOUT / ESU R: 0.434 / ESU R Free: 0.266 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.952 Å2
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Refinement step | Cycle: 1 / Resolution: 2.45→7.1 Å
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Refine LS restraints |
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