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- PDB-7p5t: Structure of CYP142 from Mycobacterium tuberculosis in complex wi... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7p5t | ||||||
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Title | Structure of CYP142 from Mycobacterium tuberculosis in complex with inhibitor MEK216 | ||||||
![]() | Steroid C26-monooxygenase | ||||||
![]() | ![]() ![]() ![]() ![]() ![]() ![]() ![]() | ||||||
Function / homology | ![]() cholesterol 26-hydroxylase activity / cholest-4-en-3-one 26-monooxygenase [(25R)-3-oxocholest-4-en-26-oate forming] / ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Snee, M. / Kavanagh, M. / Tunnicliffe, R. / McLean, K. / Levy, C. / Munro, A. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structure of CYP142 from Mycobacterium tuberculosis in complex with inhibitor MEK216 Authors: Kavanagh, M. / Coyne, A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 204.3 KB | Display | ![]() |
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PDB format | ![]() | 160.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 2xkrS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homology ![]() |
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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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 44371.238 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: cyp142, cyp142A1, Rv3518c, MTV023.25c / Production host: ![]() ![]() ![]() References: UniProt: P9WPL5, cholest-4-en-3-one 26-monooxygenase [(25R)-3-oxocholest-4-en-26-oate forming] |
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-Non-polymers , 5 types, 600 molecules ![](data/chem/img/HEM.gif)
![](data/chem/img/5YG.gif)
![](data/chem/img/BR.gif)
![](data/chem/img/K.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/5YG.gif)
![](data/chem/img/BR.gif)
![](data/chem/img/K.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-HEM / ![]() | ||||
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#3: Chemical | ChemComp-5YG / ~{ | ||||
#4: Chemical | ![]() #5: Chemical | #6: Water | ChemComp-HOH / | ![]() |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.662 Å3/Da / Density % sol: 53.82 % |
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Crystal grow![]() | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4.5 Details: 8% PEG 20,000, 8% PEG 550 MME, sodium acetate pH4.5, 0.1M potassium bromide |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 9, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.3→65.72 Å / Num. obs: 116304 / % possible obs: 99.3 % / Redundancy: 5.7 % / CC1/2: 1 / Rrim(I) all: 0.057 / Net I/σ(I): 11.4 |
Reflection shell | Resolution: 1.3→1.32 Å / Redundancy: 2.3 % / Mean I/σ(I) obs: 1 / Num. unique obs: 5347 / CC1/2: 0.566 / Rpim(I) all: 0.545 / % possible all: 91.9 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 2XKR Resolution: 1.3→64.53 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 15.51 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 84.64 Å2 / Biso mean: 25.4554 Å2 / Biso min: 11.82 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.3→64.53 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30
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